Mercurial > repos > davidmurphy > codonlogo
comparison Codonlogo.xml @ 15:981eb8c3a756 default tip
Uploaded
| author | davidmurphy |
|---|---|
| date | Sat, 31 Mar 2012 16:07:07 -0400 |
| parents | 20716450be87 |
| children |
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| 14:778f03497adb | 15:981eb8c3a756 |
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| 1 <tool id="codonlogo" name="Codon Logo" version="3"> | 1 <tool id="codonlogo" name="Codon Logo" version="3"> |
| 2 <description>generator for fasta (eg Clustal alignments)</description> | 2 <description>generator for fasta (eg Clustal alignments)</description> |
| 3 <command interpreter="python -W ignore::DeprecationWarning"> | 3 <command interpreter="python -W ignore::DeprecationWarning"> |
| 4 codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth | 4 codonlogo -F $outformat -s $size -f $input -o $output -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth |
| 5 | 5 |
| 6 #if str($logoname) != '' | |
| 7 -t "$logoname" | |
| 8 #end if | |
| 9 | |
| 6 #if str($ylabel) != '' | 10 #if str($ylabel) != '' |
| 7 -x "$xlabel" | 11 -x "$xlabel" |
| 8 #end if | 12 #end if |
| 9 | 13 |
| 10 #if str( $ylabel) != '' | 14 #if str( $ylabel) != '' |
| 330 #end if | 334 #end if |
| 331 | 335 |
| 332 </command> | 336 </command> |
| 333 <inputs> | 337 <inputs> |
| 334 <page> | 338 <page> |
| 335 <param format="text" name="input" type="data" label="Input file.(must be an aligned fasta file of sequences the same length, recommended to use sequences aligned by codon)" /> | 339 <param format="text" name="input" type="data" label="Input file." help="must be an aligned fasta file of sequences the same length, recommended to use sequences aligned by codon" /> |
| 336 | 340 |
| 337 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" /> | 341 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" /> |
| 338 | 342 |
| 339 <param name="outformat" type="select" label="Output format for image (or text report)" > | 343 <param name="outformat" type="select" label="Output format for image (or text report)" > |
| 340 <option value="png" selected="True">PNG screen quality</option> | 344 <option value="png" selected="True">PNG screen quality</option> |
| 344 <option value="eps">EPS</option> | 348 <option value="eps">EPS</option> |
| 345 <option value="txt">Text (shows the detailed calculations for each position - no image)</option> | 349 <option value="txt">Text (shows the detailed calculations for each position - no image)</option> |
| 346 </param> | 350 </param> |
| 347 <param name="resolution" size="5" type="integer" value="96" label="Bitmap resolution in dots per inch (DPI).For high quality printable PNG this should be set to 600" /> | 351 <param name="resolution" size="5" type="integer" value="96" label="Bitmap resolution in dots per inch (DPI).For high quality printable PNG this should be set to 600" /> |
| 348 | 352 |
| 349 <param name="frame" type="select" label="Frame to view the alignment. If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." > | 353 <param name="frame" type="select" label="Frame to view the alignment." help="If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." > |
| 350 <option value="0" selected="True">0</option> | 354 <option value="0" selected="True">0</option> |
| 351 <option value="1">+1</option> | 355 <option value="1">+1</option> |
| 352 <option value="2">+2</option> | 356 <option value="2">+2</option> |
| 353 <option value="3">reverse complement 0</option> | 357 <option value="3">reverse complement 0</option> |
| 354 <option value="4">reverse complement +1</option> | 358 <option value="4">reverse complement +1</option> |
| 407 <option value="none" >No small sample correction</option> | 411 <option value="none" >No small sample correction</option> |
| 408 <option value="equiprobable" >Equiprobable</option> | 412 <option value="equiprobable" >Equiprobable</option> |
| 409 <option value="Homosapiens" >Human</option> | 413 <option value="Homosapiens" >Human</option> |
| 410 <option value="Saccharomycescerevisiae" >Yeast</option> | 414 <option value="Saccharomycescerevisiae" >Yeast</option> |
| 411 <option value="Escherichiacoli" >E.Coli</option> | 415 <option value="Escherichiacoli" >E.Coli</option> |
| 412 <option value="From File">from file</option> | 416 <option value="file">from file</option> |
| 413 | 417 |
| 414 </param> | 418 </param> |
| 415 <when value="auto"> | 419 <when value="auto"> |
| 416 </when> | 420 </when> |
| 417 <when value="equiprobable"> | 421 <when value="equiprobable"> |
| 418 </when> | 422 </when> |
| 419 <when value="none"> | 423 <when value="none"> |
| 420 </when> | 424 </when> |
| 421 <when value="file"> | 425 <when value="file"> |
| 422 <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weigt." /> | 426 <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. " help="expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weight." /> |
| 423 </when> | 427 </when> |
| 424 | 428 |
| 425 </conditional> | 429 </conditional> |
| 426 <conditional name="colours"> | 430 <conditional name="colours"> |
| 427 <param name="colour" type="select" label="Choose colours?(it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc. )"> | 431 <param name="colour" type="select" label="Choose colours?" help="it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc."> |
| 428 <option value="no" selected="true">Default colours</option> | 432 <option value="no" selected="true">Default colours</option> |
| 429 <option value="part">Set your own.</option> | 433 <option value="part">Set your own.</option> |
| 430 </param> | 434 </param> |
| 431 <when value="no"> | 435 <when value="no"> |
| 432 </when> | 436 </when> |