Mercurial > repos > galaxyp > encyclopedia_searchtolib

comparison macros.xml @ 2:fb192dd6658a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 0bb79ebbaf73fe6e902f6ef20cc9c9741063bf34
author galaxyp
date Tue, 17 May 2022 14:56:17 +0000
parents 36880dfd9fa7
children
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1:36880dfd9fa7 2:fb192dd6658a
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.2.2</token> 2 <token name="@TOOL_VERSION@">1.12.34</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">encyclopedia</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">encyclopedia</requirement>
7 <yield/> 7 <yield/>
291 <option value="no">No - use default options</option> 291 <option value="no">No - use default options</option>
292 <option value="yes">Yes</option> 292 <option value="yes">Yes</option>
293 </param> 293 </param>
294 <when value="no"/> 294 <when value="no"/>
295 <when value="yes"> 295 <when value="yes">
296 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/> 296 <param argument="-percolatorVersion" type="text" value="3.01" optional="true" label="percolatorVersion">
297 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/> 297 <option value="2.10">2.10</option>
298 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> 298 <option value="3.01">3.01</option>
299 <option value="3.05">3.05</option>
300 <validator type="regex" message="Not percolator version format">^\d([.]\d+)?$</validator>
301 </param>
302 <param argument="-percolatorProteinThreshold" type="float" value="0.01" optional="true" label="percolatorProteinThreshold"/>
303 <param argument="-percolatorThreshold" type="float" value="0.01" optional="true" label="percolatorThreshold"/>
299 </when> 304 </when>
300 </conditional> 305 </conditional>
301 </xml> 306 </xml>
302 <token name="@PERCOLATOR_OPTIONS@"> 307 <token name="@PERCOLATOR_OPTIONS@">
303 #if $options.percolator.set_percolator == 'yes' 308 #if $options.percolator.set_percolator == 'yes'
304 #if str($options.percolator.percolatorVersionNumber) 309 #if str($options.percolator.percolatorVersion)
305 -percolatorVersionNumber $options.percolator.percolatorVersionNumber 310 -percolatorVersion $options.percolator.percolatorVersion
306 #end if 311 #end if
307 #if str($options.percolator.percolatorProteinThreshold) 312 #if str($options.percolator.percolatorProteinThreshold)
308 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold 313 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
309 #end if 314 #end if
310 #if str($options.percolator.percolatorThreshold) 315 #if str($options.percolator.percolatorThreshold)
311 -percolatorThreshold $options.percolator.percolatorThreshold 316 -percolatorThreshold $options.percolator.percolatorThreshold
312 #end if 317 #end if
318 #else
319 -percolatorVersion "3.01"
313 #end if 320 #end if
314 </token> 321 </token>
315 322
316 <xml name="peak_options"> 323 <xml name="peak_options">
317 <conditional name="peak"> 324 <conditional name="peak">
523 #end if 530 #end if
524 @SCAN_INPUTS@ 531 @SCAN_INPUTS@
525 @FASTA_INPUT@ 532 @FASTA_INPUT@
526 @TARGET_FASTA@ 533 @TARGET_FASTA@
527 @LIB_INPUT@ 534 @LIB_INPUT@
535 @MASS_LIBRARY_TOLERANCE@
536 @PERCOLATOR_OPTIONS@
537 @PEAK_OPTIONS@
538 @WINDOW_OPTIONS@
539 @MODIFICATION_OPTIONS@
540 @SEARCH_OPTIONS@
528 -a $a 541 -a $a
529 -o chromatogram_library.elib 542 -o chromatogram_library.elib
530 && ls -l ./*.* inputs/* 543 && ls -l ./*.* inputs/*
531 | tee -a search2lib.log 544 | tee -a search2lib.log
532 ]]> 545 ]]>