1 | item:ProbCons |
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2 | itemmeta: P |
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3 | seqtype:* |
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4 | itemmethod:(GOTO_LOCAL_DIR; \ |
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5 | arb_sed 's/#/>HASH_/' <TmpInputFile | \ |
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6 | arb_sed 's/%/>PERCENT_/' | \ |
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7 | arb_sed 's/"/>QUOTE_/'| \ |
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8 | arb_sed 's/@/>AT_/' | \ |
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9 | arb_sed '/^[^>]/ y/./-/' > probcons_in; \ |
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10 | RUN_IN_WINDOW(($ARBHOME/bin/probcons -pre $PRE_TRAINING_REPS -ir $PASSES -c $REPS probcons_in > probcons_out;)); \ |
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11 | arb_sed 's/>HASH_/#/' <probcons_out | \ |
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12 | arb_sed 's/>PERCENT_/%/' | \ |
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13 | arb_sed 's/>QUOTE_/"/' | \ |
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14 | arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(probcons_in* probcons_out* TmpInputFile) ) |
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15 | |
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16 | arg:REPS |
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17 | argtype:choice_menu |
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18 | arglabel:Passes of consistency transformation |
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19 | argtype:slider |
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20 | argmin:0 |
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21 | argmax:5 |
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22 | argvalue:2 |
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23 | |
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24 | |
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25 | arg:PASSES |
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26 | arglabel:Passes of iterative refinement |
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27 | argtype:slider |
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28 | argmin:0 |
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29 | argmax:1000 |
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30 | argvalue:100 |
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31 | |
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32 | arg:PRE_TRAINING_REPS |
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33 | arglabel:Rounds of pre-training before aligning the sequences |
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34 | argtype:slider |
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35 | argmin:0 |
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36 | argmax:20 |
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37 | argvalue:0 |
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38 | |
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39 | in:TmpInputFile |
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40 | informat:flat |
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41 | intyped:detailed |
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42 | insave: |
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43 | |
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44 | out:TmpOutputFile |
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45 | outformat:flat |
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46 | outaligned:yes |
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47 | |
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48 | //---------------------------------------------------- |
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49 | |
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50 | item:Muscle |
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51 | itemmeta: M |
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52 | seqtype:* |
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53 | itemmethod:(GOTO_LOCAL_DIR; \ |
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54 | arb_sed 's/#/>HASH_/' <TmpInputFile | \ |
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55 | arb_sed 's/%/>PERCENT_/' | \ |
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56 | arb_sed 's/"/>QUOTE_/'| \ |
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57 | arb_sed 's/@/>AT_/' | \ |
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58 | arb_sed '/^[^>]/ y/./-/' > muscle_in; \ |
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59 | RUN_IN_WINDOW(($ARBHOME/bin/muscle $SCORE $DIAGS $ANCHORS $DIMER $BRENNER -in muscle_in -out muscle_out -maxiters $MAXITERS;)); \ |
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60 | arb_sed 's/>HASH_/#/' <muscle_out | \ |
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61 | arb_sed 's/>PERCENT_/%/' | \ |
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62 | arb_sed 's/>QUOTE_/"/' | \ |
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63 | arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(muscle_in* muscle_out* TmpInputFile)) |
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64 | |
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65 | arg:MAXITERS |
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66 | argtype:text |
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67 | arglabel:Maximum number of iterations to run(Use 2 for large datasets) |
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68 | argtext:16 |
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69 | |
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70 | //arg:ANCHORS |
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71 | //argtype:choice_menu |
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72 | //arglabel:Use anchor optimization in tree dependent refinement iterations |
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73 | //argchoice:Yes(default):-anchors |
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74 | //argchoice:No:-noanchors |
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75 | |
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76 | //arg:BRENNER |
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77 | //argtype:choice_menu |
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78 | //arglabel:Use Steven Brenner's method for computing the root alignment |
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79 | //argchoice:No(default): |
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80 | //argchoice:Yes:-brenner |
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81 | |
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82 | //arg:DIMER |
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83 | //argtype:choice_menu |
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84 | //arglabel:Use dimer approximation for the SP score\n(faster, slightly less accurate) |
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85 | //argchoice:No(default): |
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86 | //argchoice:Yes:-dimer |
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87 | |
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88 | //arg:DIAGS |
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89 | //argtype:choice_menu |
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90 | //arglabel:Use diagonal optimizations\n(faster, especially for closely related sequences,\nbut may be less accurate) |
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91 | //argchoice:No(default): |
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92 | //argchoice:Yes:-diags |
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93 | |
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94 | //arg:SCORE |
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95 | //argtype:choice_menu |
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96 | //arglabel:Scoring |
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97 | //argchoice:Log-expectation profile score (VTML240)(default):-le |
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98 | //argchoice:Sum-of-pairs protein profile score (PAM200):-sp |
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99 | //argchoice:Sum-of-pairs profile score (VTML240):-sv |
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100 | |
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101 | |
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102 | in:TmpInputFile |
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103 | informat:flat |
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104 | intyped:detailed |
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105 | insave: |
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106 | |
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107 | out:TmpOutputFile |
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108 | outformat:flat |
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109 | outaligned:yes |
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110 | |
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111 | //------------------------------------------------------------------- |
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112 | |
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113 | item:Mafft |
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114 | itemmeta: f |
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115 | seqtype:* |
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116 | itemmethod:(GOTO_LOCAL_DIR; \ |
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117 | arb_sed 's/#/>HASH_/' <TmpInputFile | \ |
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118 | arb_sed 's/%/>PERCENT_/' | \ |
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119 | arb_sed 's/"/>QUOTE_/'| \ |
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120 | arb_sed 's/@/>AT_/' | \ |
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121 | arb_sed '/^[^>]/ y/./-/' > mafft_in; \ |
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122 | RUN_IN_WINDOW(($ARBHOME/bin/$COMMAND $METHOD --preservecase --ep $OFFSET $SCORING_MATRIX mafft_in > mafft_out;)); \ |
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123 | arb_sed 's/>HASH_/#/' <mafft_out | \ |
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124 | arb_sed 's/>PERCENT_/%/' | \ |
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125 | arb_sed 's/>QUOTE_/"/' | \ |
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126 | arb_sed 's/>AT_/@/' > TmpOutputFile; RM_LOCAL_FILES(mafft_in* TmpInputFile mafft_out*)) |
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127 | |
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128 | itemhelp:mafft.help |
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129 | |
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130 | |
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131 | arg:COMMAND |
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132 | argtype:choice_menu |
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133 | arglabel:Method |
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134 | argchoice:Auto:mafft --auto |
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135 | argchoice:L-INS-i:mafft-linsi |
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136 | argchoice:G-INS-i:mafft-ginsi |
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137 | argchoice:E-INS-i:mafft-einsi |
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138 | argchoice:Q-INS-i:mafft-qinsi |
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139 | argchoice:X-INS-i:mafft-xinsi |
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140 | argchoice:FFT-NS-i:mafft-fftnsi |
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141 | argchoice:FFT-NS-2:mafft-fftns |
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142 | argchoice:NW-NS-i:mafft-nwnsi |
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143 | argchoice:NW-NS-2:mafft-nwns |
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144 | |
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145 | arg:SCORING_MATRIX |
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146 | argtype:choice_menu |
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147 | arglabel:Scoring matrix |
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148 | argchoice:BLOSUM62:--bl 62 |
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149 | argchoice:BLOSUM30:--bl 30 |
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150 | argchoice:BLOSUM45:--bl 45 |
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151 | argchoice:BLOSUM80:--bl 80 |
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152 | argchoice:JTT100:--jtt 100 |
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153 | argchoice:JTT200:--jtt 200 |
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154 | argchoice:JTT200:--jtt 200 |
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155 | argchoice:1PAM / K=2:--kimura 1 |
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156 | argchoice:20PAM / K=2:--kimura 20 |
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157 | argchoice:200PAM / K=2:--kimura 200 |
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158 | |
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159 | |
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160 | arg:OFFSET |
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161 | argtype:text |
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162 | arglabel:Offset value [0..1]\n(Use Values >0.1 for closely related sequences) |
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163 | argtext:0.5 |
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164 | |
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165 | |
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166 | in:TmpInputFile |
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167 | informat:flat |
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168 | intyped:detailed |
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169 | insave: |
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170 | |
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171 | out:TmpOutputFile |
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172 | outformat:flat |
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173 | outaligned:yes |
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174 | |
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175 | //-------------------------------------------------------- |
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176 | |
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177 | item:ClustalW automatic |
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178 | itemmeta: W |
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179 | seqtype:* |
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180 | itemmethod:(GOTO_LOCAL_DIR; \ |
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181 | tr '"%//' '>' <TmpInputFile >clus_in; \ |
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182 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \ |
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183 | cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >TmpOutputFile; )); \ |
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184 | RM_LOCAL_FILES(clus_in* TmpInputFile)) |
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185 | |
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186 | itemhelp:clustalw.help |
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187 | |
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188 | |
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189 | in:TmpInputFile |
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190 | informat:flat |
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191 | insave: |
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192 | |
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193 | out:TmpOutputFile |
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194 | outformat:flat |
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195 | outaligned:yes |
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196 | |
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197 | // -------------------------------------------------------------------------------- |
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198 | |
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199 | item:Create ClustalW Profile 2 |
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200 | itemmeta: C |
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201 | seqtype:* |
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202 | itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' <TmpInputFile >../clus_prf ; RM_LOCAL_FILES(TmpInputFile)) |
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203 | |
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204 | itemhelp:clustalw.help |
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205 | |
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206 | in:TmpInputFile |
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207 | informat:flat |
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208 | insave: |
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209 | |
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210 | // -------------------------------------------------------------------------------- |
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211 | |
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212 | item:ClustalW Profile Alignment |
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213 | itemmeta: A |
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214 | seqtype:* |
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215 | itemmethod:(GOTO_LOCAL_DIR; \ |
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216 | tr '"%//' '>' <TmpInputFile >clus_in; \ |
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217 | RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \ |
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218 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )); \ |
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219 | RM_LOCAL_FILES(clus_in* TmpInputFile)) |
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220 | |
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221 | itemhelp:clustalw.help |
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222 | |
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223 | |
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224 | in:TmpInputFile |
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225 | informat:flat |
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226 | insave: |
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227 | |
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228 | out:TmpOutputFile |
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229 | outformat:flat |
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230 | outaligned:yes |
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231 | |
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232 | // -------------------------------------------------------------------------------- |
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233 | |
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234 | item:ClustalW DNA Alignment (fast) |
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235 | seqtype: N |
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236 | itemmeta: N |
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237 | itemmethod:(GOTO_LOCAL_DIR; \ |
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238 | tr '"%//' '>' <TmpInputFile >clus_in ; \ |
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239 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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240 | -quicktree $INTERACTIVE \ |
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241 | -ktuple=$KTUPLE -topdiags=$TOPDIAGS \ |
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242 | -window=$WINDOW -pairgap=$PAIRGAP \ |
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243 | -score=$SCORE \ |
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244 | -type=DNA -transweight=$TRANSWEIGHT \ |
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245 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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246 | -dnamatrix=$DNAMATRIX; \ |
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247 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | arb_sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ |
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248 | RM_LOCAL_FILES(clus_in* TmpInputFile)) |
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249 | |
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250 | itemhelp:clustalw.help |
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251 | |
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252 | // parameters for fast pairwise alignment: |
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253 | |
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254 | arg:PAIRGAP |
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255 | arglabel:Gap penalty (pairwise ali) |
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256 | argtype:slider |
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257 | argmin:1 |
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258 | argmax:500 |
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259 | argvalue:5 |
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260 | |
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261 | arg:KTUPLE |
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262 | arglabel:K-tuple size |
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263 | argtype:slider |
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264 | argmin:1 |
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265 | argmax:4 |
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266 | argvalue:2 |
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267 | |
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268 | arg:TOPDIAGS |
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269 | arglabel:No. of top diagonals |
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270 | argtype:slider |
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271 | argmin:1 |
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272 | argmax:50 |
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273 | argvalue:4 |
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274 | |
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275 | arg:WINDOW |
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276 | arglabel:Window size |
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277 | argtype:slider |
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278 | argmin:1 |
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279 | argmax:50 |
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280 | argvalue:4 |
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281 | |
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282 | // parameters for multiple alignment: |
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283 | |
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284 | arg:DNAMATRIX |
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285 | argtype:choice_menu |
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286 | arglabel:Weighting matrix (multiple ali) |
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287 | argchoice:IUB:IUB |
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288 | argchoice:CLUSTALW:CLUSTALW |
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289 | |
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290 | arg:GOP |
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291 | argtype:slider |
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292 | arglabel:Gap Open Penalty |
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293 | argmin:0 |
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294 | argmax:100 |
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295 | argvalue:15 |
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296 | |
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297 | arg:GEP |
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298 | arglabel:Gap Extend Penalty |
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299 | argtype:slider |
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300 | argmin:0 |
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301 | argmax:10 |
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302 | argvalue:6.66 |
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303 | |
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304 | arg:MAXDIV |
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305 | arglabel:% identity for delay |
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306 | argtype:slider |
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307 | argmin:0 |
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308 | argmax:100 |
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309 | argvalue:30 |
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310 | |
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311 | arg:TRANSWEIGHT |
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312 | arglabel:Transition weight |
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313 | argtype:slider |
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314 | argmin:0.0 |
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315 | argmax:1.0 |
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316 | argvalue:0.5 |
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317 | |
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318 | arg:INTERACTIVE |
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319 | arglabel:Interactive |
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320 | argtype:choice_menu |
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321 | argchoice:No: |
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322 | argchoice:Yes:-interactive |
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323 | |
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324 | in:TmpInputFile |
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325 | informat:flat |
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326 | insave: |
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327 | |
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328 | out:TmpOutputFile |
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329 | outformat:flat |
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330 | outaligned:yes |
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331 | |
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332 | // -------------------------------------------------------------------------------- |
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333 | |
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334 | item:ClustalW DNA Alignment (slow & accurate) |
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335 | seqtype: N |
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336 | itemmeta: s |
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337 | itemmethod:(GOTO_LOCAL_DIR; \ |
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338 | tr '"%//' '>' <TmpInputFile >clus_in ; \ |
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339 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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340 | $INTERACTIVE \ |
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341 | -pwdnamatrix=$PWDNAMATRIX \ |
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342 | -pwgapopen=$PWGOP -pwgapext=$PWGEP \ |
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343 | -type=DNA -transweight=$TRANSWEIGHT \ |
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344 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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345 | -dnamatrix=$DNAMATRIX; \ |
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346 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ |
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347 | RM_LOCAL_FILES(clus_in* TmpInputFile)) |
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348 | |
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349 | itemhelp:clustalw.help |
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350 | |
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351 | // parameters for pairwise alignment: |
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352 | |
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353 | arg:PWDNAMATRIX |
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354 | argtype:choice_menu |
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355 | arglabel:Weighting matrix (pairwise ali) |
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356 | argchoice:IUB:IUB |
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357 | argchoice:CLUSTALW:CLUSTALW |
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358 | |
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359 | arg:PWGOP |
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360 | argtype:slider |
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361 | arglabel:Gap Open Penalty |
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362 | argmin:0 |
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363 | argmax:100 |
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364 | argvalue:15 |
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365 | |
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366 | arg:PWGEP |
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367 | arglabel:Gap Extend Penalty |
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368 | argtype:slider |
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369 | argmin:0 |
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370 | argmax:10 |
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371 | argvalue:6.66 |
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372 | |
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373 | // parameters for multiple alignment: |
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374 | |
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375 | arg:DNAMATRIX |
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376 | argtype:choice_menu |
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377 | arglabel:Weighting matrix (multiple ali) |
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378 | argchoice:IUB:IUB |
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379 | argchoice:CLUSTALW:CLUSTALW |
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380 | |
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381 | arg:GOP |
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382 | argtype:slider |
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383 | arglabel:Gap Open Penalty |
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384 | argmin:0 |
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385 | argmax:100 |
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386 | argvalue:15 |
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387 | |
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388 | arg:GEP |
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389 | arglabel:Gap Extend Penalty |
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390 | argtype:slider |
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391 | argmin:0 |
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392 | argmax:10 |
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393 | argvalue:6.66 |
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394 | |
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395 | arg:MAXDIV |
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396 | arglabel:% identity for delay |
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397 | argtype:slider |
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398 | argmin:0 |
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399 | argmax:100 |
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400 | argvalue:30 |
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401 | |
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402 | arg:TRANSWEIGHT |
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403 | arglabel:Transition weight |
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404 | argtype:slider |
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405 | argmin:0.0 |
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406 | argmax:1.0 |
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407 | argvalue:0.5 |
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408 | |
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409 | arg:INTERACTIVE |
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410 | arglabel:Interactive |
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411 | argtype:choice_menu |
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412 | argchoice:No: |
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413 | argchoice:Yes:-interactive |
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414 | |
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415 | in:TmpInputFile |
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416 | informat:flat |
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417 | insave: |
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418 | |
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419 | out:TmpOutputFile |
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420 | outformat:flat |
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421 | outaligned:yes |
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422 | |
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423 | // -------------------------------------------------------------------------------- |
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424 | |
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425 | item:ClustalW Protein Alignment (fast) |
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426 | seqtype: A |
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427 | itemmeta: o |
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428 | itemmethod:(GOTO_LOCAL_DIR; \ |
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429 | tr '"%//' '>' <TmpInputFile >clus_in ; \ |
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430 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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431 | -quicktree $INTERACTIVE \ |
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432 | -ktuple=$KTUPLE -topdiags=$TOPDIAGS \ |
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433 | -window=$WINDOW -pairgap=$PAIRGAP \ |
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434 | -score=$SCORE \ |
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435 | -type=PROTEIN -transweight=$TRANSWEIGHT \ |
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436 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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437 | -matrix=$MATRIX $NEGMATRIX; \ |
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438 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ |
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439 | RM_LOCAL_FILES(clus_in* TmpInputFile)) |
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440 | |
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441 | itemhelp:clustalw.help |
---|
442 | |
---|
443 | // parameters for fast pairwise alignment: |
---|
444 | |
---|
445 | arg:PAIRGAP |
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446 | arglabel:Gap penalty (pairwise ali) |
---|
447 | argtype:slider |
---|
448 | argmin:1 |
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449 | argmax:500 |
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450 | argvalue:3 |
---|
451 | |
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452 | arg:KTUPLE |
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453 | arglabel:K-tuple size |
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454 | argtype:slider |
---|
455 | argmin:1 |
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456 | argmax:2 |
---|
457 | argvalue:1 |
---|
458 | |
---|
459 | arg:TOPDIAGS |
---|
460 | arglabel:No. of top diagonals |
---|
461 | argtype:slider |
---|
462 | argmin:1 |
---|
463 | argmax:50 |
---|
464 | argvalue:5 |
---|
465 | |
---|
466 | arg:WINDOW |
---|
467 | arglabel:Window size |
---|
468 | argtype:slider |
---|
469 | argmin:1 |
---|
470 | argmax:50 |
---|
471 | argvalue:5 |
---|
472 | |
---|
473 | // parameters for multiple alignment: |
---|
474 | |
---|
475 | arg:MATRIX |
---|
476 | argtype:choice_menu |
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477 | arglabel:Weighting matrix (multiple ali) |
---|
478 | argchoice:Gonnet series:GONNET |
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479 | argchoice:Blosum series:BLOSUM |
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480 | argchoice:PAM series:PAM |
---|
481 | argchoice:ID matrix:ID |
---|
482 | |
---|
483 | arg:GOP |
---|
484 | argtype:slider |
---|
485 | arglabel:Gap Open Penalty |
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486 | argmin:0 |
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487 | argmax:100 |
---|
488 | argvalue:10 |
---|
489 | |
---|
490 | arg:GEP |
---|
491 | arglabel:Gap Extend Penalty |
---|
492 | argtype:slider |
---|
493 | argmin:0 |
---|
494 | argmax:10 |
---|
495 | argvalue:0.2 |
---|
496 | |
---|
497 | arg:MAXDIV |
---|
498 | arglabel:% identity for delay |
---|
499 | argtype:slider |
---|
500 | argmin:0 |
---|
501 | argmax:100 |
---|
502 | argvalue:30 |
---|
503 | |
---|
504 | arg:TRANSWEIGHT |
---|
505 | arglabel:Transition weight |
---|
506 | argtype:slider |
---|
507 | argmin:0.0 |
---|
508 | argmax:1.0 |
---|
509 | argvalue:0.5 |
---|
510 | |
---|
511 | arg:NEGMATRIX |
---|
512 | arglabel:Use negative matrix |
---|
513 | argtype:choice_menu |
---|
514 | argchoice:No: |
---|
515 | argchoice:Yes:-negative |
---|
516 | |
---|
517 | arg:INTERACTIVE |
---|
518 | arglabel:Interactive |
---|
519 | argtype:choice_menu |
---|
520 | argchoice:No: |
---|
521 | argchoice:Yes:-interactive |
---|
522 | |
---|
523 | in:TmpInputFile |
---|
524 | informat:flat |
---|
525 | insave: |
---|
526 | |
---|
527 | out:TmpOutputFile |
---|
528 | outformat:flat |
---|
529 | outaligned:yes |
---|
530 | |
---|
531 | // -------------------------------------------------------------------------------- |
---|
532 | |
---|
533 | item:ClustalW Protein Alignment (slow & accurate) |
---|
534 | seqtype: A |
---|
535 | itemmeta: l |
---|
536 | itemmethod:(GOTO_LOCAL_DIR; \ |
---|
537 | tr '"%//' '>' <TmpInputFile >clus_in ; \ |
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538 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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539 | $INTERACTIVE \ |
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540 | -pwmatrix=$PWMATRIX \ |
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541 | -pwgapopen=$PWGOP -pwgapext=$PWGEP \ |
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542 | -type=PROTEIN -transweight=$TRANSWEIGHT \ |
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543 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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544 | -matrix=$MATRIX $NEGMATRIX; \ |
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545 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >TmpOutputFile; )) ; \ |
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546 | RM_LOCAL_FILES(clus_in* TmpInputFile)) |
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547 | |
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548 | itemhelp:clustalw.help |
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549 | |
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550 | // parameters for pairwise alignment: |
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551 | |
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552 | arg:PWMATRIX |
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553 | argtype:choice_menu |
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554 | arglabel:Weighting matrix (pairwise ali) |
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555 | argchoice:Gonnet series:GONNET |
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556 | argchoice:Blosum series:BLOSUM |
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557 | argchoice:PAM series:PAM |
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558 | argchoice:ID matrix:ID |
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559 | |
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560 | arg:PWGOP |
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561 | argtype:slider |
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562 | arglabel:Gap Open Penalty |
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563 | argmin:0 |
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564 | argmax:100 |
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565 | argvalue:10 |
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566 | |
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567 | arg:PWGEP |
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568 | arglabel:Gap Extend Penalty |
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569 | argtype:slider |
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570 | argmin:0 |
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571 | argmax:10 |
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572 | argvalue:0.1 |
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573 | |
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574 | // parameters for multiple alignment: |
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575 | |
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576 | arg:MATRIX |
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577 | argtype:choice_menu |
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578 | arglabel:Weighting matrix (multiple ali) |
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579 | argchoice:Gonnet series:GONNET |
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580 | argchoice:Blosum series:BLOSUM |
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581 | argchoice:PAM series:PAM |
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582 | argchoice:ID matrix:ID |
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583 | |
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584 | arg:GOP |
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585 | argtype:slider |
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586 | arglabel:Gap Open Penalty |
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587 | argmin:0 |
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588 | argmax:100 |
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589 | argvalue:10 |
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590 | |
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591 | arg:GEP |
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592 | arglabel:Gap Extend Penalty |
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593 | argtype:slider |
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594 | argmin:0 |
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595 | argmax:10 |
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596 | argvalue:0.2 |
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597 | |
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598 | arg:MAXDIV |
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599 | arglabel:% identity for delay |
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600 | argtype:slider |
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601 | argmin:0 |
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602 | argmax:100 |
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603 | argvalue:30 |
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604 | |
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605 | arg:TRANSWEIGHT |
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606 | arglabel:Transition weight |
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607 | argtype:slider |
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608 | argmin:0.0 |
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609 | argmax:1.0 |
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610 | argvalue:0.5 |
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611 | |
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612 | arg:NEGMATRIX |
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613 | arglabel:Use negative matrix |
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614 | argtype:choice_menu |
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615 | argchoice:No: |
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616 | argchoice:Yes:-negative |
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617 | |
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618 | arg:INTERACTIVE |
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619 | arglabel:Interactive |
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620 | argtype:choice_menu |
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621 | argchoice:No: |
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622 | argchoice:Yes:-interactive |
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623 | |
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624 | in:TmpInputFile |
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625 | informat:flat |
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626 | insave: |
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627 | |
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628 | out:TmpOutputFile |
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629 | outformat:flat |
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630 | outaligned:yes |
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631 | |
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632 | // -------------------------------------------------------------------------------- |
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633 | |
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634 | item:Assemble Contigs |
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635 | itemmeta: g |
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636 | seqtype:* |
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637 | itemmethod: ( GOTO_LOCAL_DIR; \ |
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638 | tr '"%//' '>' <TmpInputFile > tr.out; \ |
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639 | CAP2 tr.out $OVERLAP $PMATCH > TmpOutputFile; \ |
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640 | RM_LOCAL_FILES(TmpInputFile tr.out) ) |
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641 | itemhelp:CAP2.help |
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642 | |
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643 | arg:OVERLAP |
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644 | argtype:slider |
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645 | arglabel:Minimum overlap? |
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646 | argmin:5 |
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647 | argmax:100 |
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648 | argvalue:20 |
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649 | |
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650 | arg:PMATCH |
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651 | argtype:slider |
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652 | arglabel:Percent match required within overlap |
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653 | argmin:25 |
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654 | argmax:100 |
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655 | argvalue:90 |
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656 | |
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657 | in:TmpInputFile |
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658 | informat:flat |
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659 | insave: |
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660 | |
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661 | out:TmpOutputFile |
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662 | outformat:gde |
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663 | |
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