Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 46:baeced706dbc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
author galaxyp
date Wed, 11 Jul 2018 08:14:23 -0400
parents 5fa8b409599e
children 58a3e6cb2598
comparison
equal deleted inserted replaced
45:5fa8b409599e 46:baeced706dbc
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.20"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26">
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="1.16.20">peptide-shaker</requirement> 9 <requirement type="package" version="1.16.26">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
353 <filter>'7' in outputs</filter> 353 <filter>'7' in outputs</filter>
354 </data> 354 </data>
355 </outputs> 355 </outputs>
356 <tests> 356 <tests>
357 <test> 357 <test>
358 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 358 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
359 <param name="processing_options_selector" value="no"/> 359 <param name="processing_options_selector" value="no"/>
360 <param name="filtering_options_selector" value="no"/> 360 <param name="filtering_options_selector" value="no"/>
361 <param name="outputs" value="zip,3"/> 361 <param name="outputs" value="zip,3"/>
362 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> 362 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
363 <output name="output_psm"> 363 <output name="output_psm">
364 <assert_contents> 364 <assert_contents>
365 <has_text text="cds.comp41779_c0_seq1" /> 365 <has_text text="cds.comp41779_c0_seq1" />
366 </assert_contents> 366 </assert_contents>
367 </output> 367 </output>
368 </test> 368 </test>
369 <test> 369 <test>
370 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 370 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
371 <param name="processing_options_selector" value="no"/> 371 <param name="processing_options_selector" value="no"/>
372 <param name="filtering_options_selector" value="yes"/> 372 <param name="filtering_options_selector" value="yes"/>
373 <param name="min_peptide_length" value="1"/> 373 <param name="min_peptide_length" value="1"/>
374 <param name="outputs" value="0,1,2,3,4,5,6,7"/> 374 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
375 <output name="output_certificate"> 375 <output name="output_certificate">
419 <has_text text="cds.comp41779_c0_seq1" /> 419 <has_text text="cds.comp41779_c0_seq1" />
420 </assert_contents> 420 </assert_contents>
421 </output> 421 </output>
422 </test> 422 </test>
423 <test> 423 <test>
424 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 424 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
425 <param name="processing_options_selector" value="no"/> 425 <param name="processing_options_selector" value="no"/>
426 <param name="filtering_options_selector" value="no"/> 426 <param name="filtering_options_selector" value="no"/>
427 <param name="outputs" value="3,cps"/> 427 <param name="outputs" value="3,cps"/>
428 <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/> 428 <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
429 <output name="output_psm"> 429 <output name="output_psm">
430 <assert_contents> 430 <assert_contents>
431 <has_text text="cds.comp41779_c0_seq1" /> 431 <has_text text="cds.comp41779_c0_seq1" />
432 </assert_contents> 432 </assert_contents>
433 </output> 433 </output>