Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 24:815f93bb3e1b draft

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author galaxyp
date Fri, 06 Nov 2015 15:33:34 -0500
parents e3be595c0bf5
children 0986f68fb410
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23:913dbf2b83e0 24:815f93bb3e1b
1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1">
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="0.40">peptide_shaker</requirement> 9 <requirement type="package" version="1.1">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
31 -temp_folder \$cwd/PeptideShakerCLI 31 -temp_folder \$cwd/PeptideShakerCLI
32 -experiment '$exp_str' 32 -experiment '$exp_str'
33 -sample '$samp_str' 33 -sample '$samp_str'
34 -replicate 1 34 -replicate 1
35 -identification_files \$cwd/searchgui_input.zip 35 -identification_files \$cwd/searchgui_input.zip
36 -out \$cwd/peptideshaker_output.cps 36 -out \$cwd/peptideshaker_output.cpsx
37 -zip \$cwd/peptideshaker_output.zip 37 -zip \$cwd/peptideshaker_output.zip
38 38
39 -threads "\${GALAXY_SLOTS:-12}" 39 -threads "\${GALAXY_SLOTS:-12}"
40 40
41 ##Optional gene annotation parameter 41 ##Optional gene annotation parameter
164 164
165 ]]> 165 ]]>
166 </command> 166 </command>
167 <inputs> 167 <inputs>
168 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" 168 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
169 help="SearchGUI Results from History"/> 169 help="SearchGUI Results from History">
170 <options options_filter_attribute="metadata.searchgui_major_version" >
171 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
172 </options>
173 <validator type="expression" message="This version of PeptideShaker will only work with SearchGUI version: @SEARCHGUI_MAJOR_VERSION@ .">value is not None and value.metadata.searchgui_major_version == "@SEARCHGUI_MAJOR_VERSION@"</validator>
174 </param>
170 175
171 <conditional name="species_type"> 176 <conditional name="species_type">
172 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" 177 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
173 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"> 178 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">
174 <option value="Fungi">Fungi</option> 179 <option value="Fungi">Fungi</option>
176 <option value="Metazoa">Metazoa</option> 181 <option value="Metazoa">Metazoa</option>
177 <option value="Vertebrates">Vertebrates</option> 182 <option value="Vertebrates">Vertebrates</option>
178 <option value="Protists">Protists</option> 183 <option value="Protists">Protists</option>
179 <option value="no_species_type" selected="true">No species restriction</option> 184 <option value="no_species_type" selected="true">No species restriction</option>
180 </param> 185 </param>
186 <when value="no_species_type"/>
181 <when value="Protists"> 187 <when value="Protists">
182 <param name="species" type="select" label="The species to use for the gene annotation" 188 <param name="species" type="select" label="The species to use for the gene annotation"
183 help=""> 189 help="">
184 <option value="Albugo laibachii">Albugo laibachii</option> 190 <option value="Albugo laibachii">Albugo laibachii</option>
185 <option value="Bigelowiella natans">Bigelowiella natans</option> 191 <option value="Bigelowiella natans">Bigelowiella natans</option>