Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 29:78fad25eff17 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
author galaxyp
date Fri, 10 Jun 2016 09:58:03 -0400
parents 432140bcc7fe
children ad60446b1e93
comparison
equal deleted inserted replaced
28:432140bcc7fe 29:78fad25eff17
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.10.0"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0">
2 <description> 2 <description>
3 Perform protein identification using various search engines based on results from SearchGUI 3 Perform protein identification using various search engines based on results from SearchGUI
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="1.10">peptide_shaker</requirement> 9 <requirement type="package" version="1.11">peptide_shaker</requirement>
10 </requirements> 10 </requirements>
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <command> 12 <command>
13 <![CDATA[ 13 <![CDATA[
14 #from datetime import datetime 14 #from datetime import datetime
56 #if str($processing_options.ptm_score.ptm_threshold) != '' 56 #if str($processing_options.ptm_score.ptm_threshold) != ''
57 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" 57 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
58 #end if 58 #end if
59 #end if 59 #end if
60 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" 60 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
61 -ptm_alignment "${processing_options.ptm_alignment}"
61 #end if 62 #end if
62 63
63 ##Optional filtering parameters: 64 ##Optional filtering parameters:
64 #if $filtering_options.filtering_options_selector == "yes": 65 #if $filtering_options.filtering_options_selector == "yes":
65 -import_peptide_length_min "${filtering_options.min_peptide_length}" 66 -import_peptide_length_min "${filtering_options.min_peptide_length}"
474 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> 475 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
475 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" 476 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
476 help="Automatic mode will be used if not set" /> 477 help="Automatic mode will be used if not set" />
477 </when> 478 </when>
478 </conditional> 479 </conditional>
480 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
479 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> 481 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
480 </when> 482 </when>
481 </conditional> 483 </conditional>
482 <conditional name="filtering_options"> 484 <conditional name="filtering_options">
483 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options" 485 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"