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comparison peptide_shaker.xml @ 38:79e37eff006d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6
author galaxyp
date Wed, 24 May 2017 21:35:25 -0400
parents 7f2aeb19650f
children f35bb9d0c93e
comparison
equal deleted inserted replaced
37:7f2aeb19650f 38:79e37eff006d
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.3"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.4">
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="1.16.3">peptide-shaker</requirement> 9 <requirement type="package" version="1.16.4">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
49 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" 49 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
50 #if str($processing_options.ptm_score.ptm_threshold) != '' 50 #if str($processing_options.ptm_score.ptm_threshold) != ''
51 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" 51 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
52 #end if 52 #end if
53 #end if 53 #end if
54 -ptm_alignment "${processing_options.ptm_alignment}"
55 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
54 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" 56 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
55 -ptm_alignment "${processing_options.ptm_alignment}"
56 #end if 57 #end if
57 58
58 ##Optional filtering parameters: 59 ##Optional filtering parameters:
59 #if $filtering_options.filtering_options_selector == "yes": 60 #if $filtering_options.filtering_options_selector == "yes":
60 -import_peptide_length_min "${filtering_options.min_peptide_length}" 61 -import_peptide_length_min "${filtering_options.min_peptide_length}"
203 help="default 95%: '95.0'" /> 204 help="default 95%: '95.0'" />
204 <conditional name="ptm_score"> 205 <conditional name="ptm_score">
205 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> 206 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
206 <option value="0" selected="True">A-score</option> 207 <option value="0" selected="True">A-score</option>
207 <option value="1">PhosphoRS</option> 208 <option value="1">PhosphoRS</option>
209 <option value="2">None</option>
208 </param> 210 </param>
209 <when value="0" /> 211 <when value="0" />
210 <when value="1"> 212 <when value="1">
211 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> 213 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
212 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" 214 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
213 help="Automatic mode will be used if not set" /> 215 help="Automatic mode will be used if not set" />
214 </when> 216 </when>
217 <when value="2" />
215 </conditional> 218 </conditional>
219 <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
220 <option value="0">Character Sequence</option>
221 <option value="1" selected="true">Amino Acids</option>
222 <option value="2">Indistinguishable Amino Acids</option>
223 </param>
216 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> 224 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
217 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> 225 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
218 </when> 226 </when>
219 </conditional> 227 </conditional>
220 <conditional name="filtering_options"> 228 <conditional name="filtering_options">