Mercurial > repos > davidmurphy > codonlogo
comparison Codonlogo.xml @ 8:5149eb3a89c2
Uploaded
| author | davidmurphy |
|---|---|
| date | Fri, 20 Jan 2012 09:03:40 -0500 |
| parents | 4d47ab2b7bcc |
| children | f3462128e87c |
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| 7:8d676bbd1f2d | 8:5149eb3a89c2 |
|---|---|
| 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="/usr/tmp/bin/python2.7 -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 | 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 $scalewidth |
| 5 | 5 |
| 6 #if str($ylabel) != '' | 6 #if str($ylabel) != '' |
| 7 -x $xlabel | 7 -x "$xlabel" |
| 8 #end if | 8 #end if |
| 9 | 9 |
| 10 #if str( $ylabel) != '' | 10 #if str( $ylabel) != '' |
| 11 -y $ylabel | 11 -y "$ylabel" |
| 12 #end if | 12 #end if |
| 13 #if $range.mode == 'part' | 13 |
| 14 #if str($range.mode) == 'part' | |
| 14 -l "$range.seqstart" -u "$range.seqend" | 15 -l "$range.seqstart" -u "$range.seqend" |
| 15 #end if | 16 #end if |
| 16 #if $comp.mode == 'equiprobable' | 17 #if str($comp.mode) == 'equiprobable' |
| 17 --composition 'equiprobable' | 18 --composition 'equiprobable' |
| 18 #end if | 19 #end if |
| 19 #if $comp.mode == 'none' | 20 #if str($comp.mode) == 'none' |
| 20 --composition 'none' | 21 --composition 'none' |
| 21 #end if | 22 #end if |
| 22 #if $comp.mode == 'file' | 23 #if str($comp.mode) == 'file' |
| 23 -R $compfile | 24 -R $compfile |
| 25 #end if | |
| 26 #if str($comp.mode) == 'Escherichiacoli' | |
| 27 -R Escherichiacoli.txt | |
| 28 #end if | |
| 29 #if str($comp.mode) == 'Saccharomycescerevisiae' | |
| 30 -R Saccharomycescerevisiae.txt | |
| 31 #end if | |
| 32 #if str($comp.mode) == 'Homosapiens' | |
| 33 -R Homosapiens.txt | |
| 24 #end if | 34 #end if |
| 25 | 35 |
| 26 #if $colours.colour == 'part' | 36 #if $colours.colour == 'part' |
| 27 | 37 |
| 28 #if str( $colours.colorAAA) != '' | 38 #if str( $colours.colorAAA) != '' |
| 320 #end if | 330 #end if |
| 321 | 331 |
| 322 </command> | 332 </command> |
| 323 <inputs> | 333 <inputs> |
| 324 <page> | 334 <page> |
| 325 <param format="fasta" name="input" type="data" label="txt" /> | 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)" /> |
| 326 | 336 |
| 327 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" /> | 337 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" /> |
| 328 | 338 |
| 329 <param name="outformat" type="select" label="Output format for image (or text report)" > | 339 <param name="outformat" type="select" label="Output format for image (or text report)" > |
| 330 <option value="png" selected="True">PNG screen quality</option> | 340 <option value="png" selected="True">PNG screen quality</option> |
| 332 <option value="pdf">PDF</option> | 342 <option value="pdf">PDF</option> |
| 333 <option value="jpeg">JPG</option> | 343 <option value="jpeg">JPG</option> |
| 334 <option value="eps">EPS</option> | 344 <option value="eps">EPS</option> |
| 335 <option value="txt">Text (shows the detailed calculations for each position - no image)</option> | 345 <option value="txt">Text (shows the detailed calculations for each position - no image)</option> |
| 336 </param> | 346 </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" /> | |
| 348 | |
| 337 <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." > | 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." > |
| 338 <option value="0" selected="True">0</option> | 350 <option value="0" selected="True">0</option> |
| 339 <option value="1">+1</option> | 351 <option value="1">+1</option> |
| 340 <option value="2">-1</option> | 352 <option value="2">+2</option> |
| 341 <option value="3">reverse complement 0</option> | 353 <option value="3">reverse complement 0</option> |
| 342 <option value="4">reverse complement +1</option> | 354 <option value="4">reverse complement +1</option> |
| 343 <option value="5">reverse complement -1</option> | 355 <option value="5">reverse complement +2</option> |
| 344 </param> | 356 </param> |
| 345 <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" /> | 357 <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" /> |
| 346 <param name="showxaxis" type="select" display="radio" label="Display sequence numbers along x-axis?" > | 358 <param name="showxaxis" type="select" display="radio" label="Display sequence numbers along x-axis?" > |
| 347 <option value="True" selected="True">Yes</option> | 359 <option value="True" selected="True">Yes</option> |
| 348 <option value="False">No</option> | 360 <option value="False">No</option> |
| 349 </param> | 361 </param> |
| 350 <param name="xlabel" label="X-axis label" type="text" size="50" value="" /> | 362 <param name="xlabel" label="X-axis label" type="text" size="50" value="" /> |
| 351 <param name="ylabel" label="Y-axis label" type="text" size="50" value="" /> | 363 <param name="ylabel" label="Y-axis label" type="text" size="50" value="" /> |
| 352 | 364 |
| 353 <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.0" /> | 365 <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.1" /> |
| 354 | 366 |
| 355 | 367 <param name="stackwidth" size="5" type="float" value="40.0" label="Width of a logo stack" /> |
| 368 | |
| 369 <param name="stackheight" size="5" type="integer" value="100" label="height of a logo stack" /> | |
| 370 <param name="box" type="select" display="radio" label="Draw boxes around symbols?" > | |
| 371 <option value="True" >Yes</option> | |
| 372 <option value="False" selected="True">No</option> | |
| 373 </param> | |
| 356 <param name="showyaxis" type="select" display="radio" label="Display entropy scale along y-axis?" > | 374 <param name="showyaxis" type="select" display="radio" label="Display entropy scale along y-axis?" > |
| 357 <option value="True" selected="True">Yes</option> | 375 <option value="True" selected="True">Yes</option> |
| 358 <option value="False">No</option> | 376 <option value="False">No</option> |
| 359 </param> | 377 </param> |
| 360 <param name="errorbars" type="select" display="radio" label="Display error bars?" > | 378 <param name="errorbars" type="select" display="radio" label="Display error bars?" > |
| 361 <option value="True" selected="True">Yes</option> | 379 <option value="True" selected="True">Yes</option> |
| 362 <option value="False">No</option> | 380 <option value="False">No</option> |
| 381 </param> | |
| 382 <param name="scalewidth" type="select" display="radio" label="Scale the visible stack width by the fraction of symbols in the column?" > | |
| 383 <option value="True" selected="True">Yes</option> | |
| 384 <option value="False">No</option> | |
| 385 </param> | |
| 386 <param name="strict" type="select" display="radio" label="Allow gaps which are not in groups of 3/ allow codons with ambiguous nucleotides." > | |
| 387 <option value="False" selected="True">Yes</option> | |
| 388 <option value="True" >No</option> | |
| 363 </param> | 389 </param> |
| 364 <conditional name="range"> | 390 <conditional name="range"> |
| 365 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> | 391 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> |
| 366 <option value="complete" selected="true">complete sequence</option> | 392 <option value="complete" selected="true">complete sequence</option> |
| 367 <option value="part">Only use a part of the sequence</option> | 393 <option value="part">Only use a part of the sequence</option> |
| 368 </param> | 394 </param> |
| 369 <when value="complete"> | 395 <when value="complete"> |
| 370 </when> | 396 </when> |
| 371 <when value="part"> | 397 <when value="part"> |
| 372 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" | 398 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying codon numbers outside the sequence lengths will cause unpredictable but bad consequences!" |
| 373 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> | 399 label="Index_start (eg 1=first codon) of the start of the sequence range to include in the logo"> |
| 374 </param> | 400 </param> |
| 375 <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" > | 401 <param name="seqend" size="5" type="integer" value="99999" label="Index_end (eg 75=75th codon) of the end of the sequence range to include in the logo" > |
| 376 </param> | 402 </param> |
| 377 </when> | 403 </when> |
| 378 </conditional> | 404 </conditional> |
| 379 <conditional name="comp"> | 405 <conditional name="comp"> |
| 380 <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file"> | 406 <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file"> |
| 381 | 407 |
| 382 <option value="equiprobable" >equiprobable</option> | 408 <option value="equiprobable" >equiprobable</option> |
| 383 <option value="none" >none</option> | 409 <option value="none" >none</option> |
| 410 <!-- <option value="Escherichiacoli" >Escherichiacoli</option> | |
| 411 <option value="Homosapiens" >Homosapiens</option> | |
| 412 <option value="Saccharomycescerevisiae" >Saccharomycescerevisiae</option>--> | |
| 384 <option value="file">from file</option> | 413 <option value="file">from file</option> |
| 385 | 414 |
| 386 </param> | 415 </param> |
| 387 <when value="auto"> | 416 <when value="auto"> |
| 388 </when> | 417 </when> |