Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 21:dfaea053e32f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
author iracooke
date Tue, 16 Jun 2015 23:43:39 -0400
parents 2cafc729b2ae
children e3be595c0bf5
comparison
equal deleted inserted replaced
20:2cafc729b2ae 21:dfaea053e32f
1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0">
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 <requirements>
6 <requirement type="package" version="0.38">peptide_shaker</requirement>
7 </requirements>
8 <macros> 5 <macros>
9 <import>macros.xml</import> 6 <import>macros.xml</import>
10 </macros> 7 </macros>
8 <requirements>
9 <requirement type="package" version="0.40">peptide_shaker</requirement>
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
15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
159 (exit \$exit_code_for_galaxy) 159 (exit \$exit_code_for_galaxy)
160 160
161 ]]> 161 ]]>
162 </command> 162 </command>
163 <inputs> 163 <inputs>
164 <param name="searchgui_input" format="searchgui_zip" type="data" label="Compressed SearchGUI results" 164 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
165 help="SearchGUI Results from History"/> 165 help="SearchGUI Results from History"/>
166 166
167 <conditional name="species_type"> 167 <conditional name="species_type">
168 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" 168 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
169 help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results"> 169 help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results">
543 <filter>'7' in outputs</filter> 543 <filter>'7' in outputs</filter>
544 </data> 544 </data>
545 </outputs> 545 </outputs>
546 <tests> 546 <tests>
547 <test> 547 <test>
548 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> 548 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
549 <param name="species_type_selector" value="no_species_type"/> 549 <param name="species_type_selector" value="no_species_type"/>
550 <param name="processing_options_selector" value="no"/> 550 <param name="processing_options_selector" value="no"/>
551 <param name="filtering_options_selector" value="no"/> 551 <param name="filtering_options_selector" value="no"/>
552 <param name="outputs" value="zip,cps,3"/> 552 <param name="outputs" value="zip,cps,3"/>
553 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> 553 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" />
554 <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" /> 554 <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" />
555 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> 555 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
556 </test> 556 </test>
557 <test> 557 <test>
558 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> 558 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
559 <param name="species_type_selector" value="no_species_type"/> 559 <param name="species_type_selector" value="no_species_type"/>
560 <param name="processing_options_selector" value="no"/> 560 <param name="processing_options_selector" value="no"/>
561 <param name="filtering_options_selector" value="yes"/> 561 <param name="filtering_options_selector" value="yes"/>
562 <param name="min_peptide_length" value="1"/> 562 <param name="min_peptide_length" value="1"/>
563 <param name="outputs" value="0,1,2,3,4,5,6,7"/> 563 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
564 <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/> 564 <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/>
565 <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> 565 <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" />
566 <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> 566 <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" />
567 <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> 567 <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" />
568 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> 568 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" />
569 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> 569 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" />
570 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> 570 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" />
571 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> 571 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
572 </test> 572 </test>
573 <test> 573 <test>
574 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> 574 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
575 <param name="species_type_selector" value="Vertebrates"/> 575 <param name="species_type_selector" value="Vertebrates"/>
576 <param name="species" value="Human (Homo sapiens)"/> 576 <param name="species" value="Human (Homo sapiens)"/>
577 <param name="processing_options_selector" value="no"/> 577 <param name="processing_options_selector" value="no"/>
578 <param name="filtering_options_selector" value="yes"/> 578 <param name="filtering_options_selector" value="yes"/>
579 <param name="min_peptide_length" value="1"/> 579 <param name="min_peptide_length" value="1"/>