Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 33:bce45e9e6d70 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
author galaxyp
date Mon, 06 Feb 2017 21:53:07 -0500
parents ff592231f118
children 0ebf3d3e4c90
comparison
equal deleted inserted replaced
32:ff592231f118 33:bce45e9e6d70
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.14.6">
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="1.13.6">peptide-shaker</requirement> 9 <requirement type="package" version="1.14.6">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
80 #if 'mzidentML' in str($outputs).split(','): 80 #if 'mzidentML' in str($outputs).split(','):
81 echo "Generating mzIdentML"; 81 echo "Generating mzIdentML";
82 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI 82 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
83 --exec_dir="\$cwd/${bin_dir}" 83 --exec_dir="\$cwd/${bin_dir}"
84 -in \$cwd/peptideshaker_output.zip 84 -in \$cwd/peptideshaker_output.zip
85 -output_file output.mzid 85 -output_file \$cwd/output.mzid
86 #if $contact_options.contact_options_selector == "yes": 86 #if $contact_options.contact_options_selector == "yes":
87 -contact_first_name "$contact_options.contact_first_name" 87 -contact_first_name "$contact_options.contact_first_name"
88 -contact_last_name "$contact_options.contact_last_name" 88 -contact_last_name "$contact_options.contact_last_name"
89 -contact_email "$contact_options.contact_email" 89 -contact_email "$contact_options.contact_email"
90 -contact_address "$contact_options.contact_address" 90 -contact_address "$contact_options.contact_address"
335 <test> 335 <test>
336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
337 <param name="processing_options_selector" value="no"/> 337 <param name="processing_options_selector" value="no"/>
338 <param name="filtering_options_selector" value="no"/> 338 <param name="filtering_options_selector" value="no"/>
339 <param name="outputs" value="zip,3"/> 339 <param name="outputs" value="zip,3"/>
340 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" /> 340 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
341 <output name="output_psm"> 341 <output name="output_psm">
342 <assert_contents> 342 <assert_contents>
343 <has_text text="cds.comp41779_c0_seq1" /> 343 <has_text text="cds.comp41779_c0_seq1" />
344 </assert_contents> 344 </assert_contents>
345 </output> 345 </output>
356 <has_text text="Carbamidomethylation of C" /> 356 <has_text text="Carbamidomethylation of C" />
357 </assert_contents> 357 </assert_contents>
358 </output> 358 </output>
359 <output name="output_hierarchical"> 359 <output name="output_hierarchical">
360 <assert_contents> 360 <assert_contents>
361 <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" /> 361 <has_text_matching expression="1.1\tcds.comp" />
362 </assert_contents> 362 </assert_contents>
363 </output> 363 </output>
364 <output name="output_psm"> 364 <output name="output_psm">
365 <assert_contents> 365 <assert_contents>
366 <not_has_text text="Phosphosite" /> 366 <not_has_text text="Phosphosite" />