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comparison peptide_shaker.xml @ 44:f35bb9d0c93e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 05:09:36 -0400
parents 79e37eff006d
children 5fa8b409599e
comparison
equal deleted inserted replaced
43:7963340ab569 44:f35bb9d0c93e
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.4"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.17">
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="1.16.4">peptide-shaker</requirement> 9 <requirement type="package" version="1.16.17">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
34 -replicate 1 34 -replicate 1
35 -identification_files \$cwd/searchgui_input.zip 35 -identification_files \$cwd/searchgui_input.zip
36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par 36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
37 -out \$cwd/peptideshaker_output.cpsx 37 -out \$cwd/peptideshaker_output.cpsx
38 -zip \$cwd/peptideshaker_output.zip 38 -zip \$cwd/peptideshaker_output.zip
39 #set $cleaned_list = str($outputs).split(',')
40 #if 'cps' in $cleaned_list:
41 #silent $cleaned_list.remove('cps')
42 #end if
43 #if 'mzidentML' in $cleaned_list:
44 #silent $cleaned_list.remove('mzidentML')
45 #end if
46 #if 'zip' in $cleaned_list:
47 #silent $cleaned_list.remove('zip')
48 #end if
49 #if len($cleaned_list) > 0
50 ## Only numbers are left over. These corresponds to different reports.
51 -reports #echo ','.join($cleaned_list)#
52 #end if
39 53
40 -threads "\${GALAXY_SLOTS:-12}" 54 -threads "\${GALAXY_SLOTS:-12}"
41 55
42 ##Optional processing parameters: 56 ##Optional processing parameters:
43 #if $processing_options.processing_options_selector == "yes" 57 #if $processing_options.processing_options_selector == "yes"
105 -contact_address "galaxyp@umn.edu" 119 -contact_address "galaxyp@umn.edu"
106 -organization_name "University of Minnesota" 120 -organization_name "University of Minnesota"
107 -organization_email "galaxyp@umn.edu" 121 -organization_email "galaxyp@umn.edu"
108 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten" 122 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
109 #end if 123 #end if
110 2>> $temp_stderr) 124 2>> $temp_stderr)
111 && 125 &&
112 #end if 126 #end if
113 127
114 ## Generate Reports if the user has selected one of the 8 additional reports 128 ## Generate Reports if the user has selected one of the 8 additional reports
115 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 129 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
116 ## and will not be passed to the command line 130 ## and will not be passed to the command line
117 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): 131 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
118 132
119 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI 133 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
120 --exec_dir="\$cwd/${bin_dir}" 134 --exec_dir="\$cwd/${bin_dir}"
303 </inputs> 317 </inputs>
304 <outputs> 318 <outputs>
305 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> 319 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
306 <filter>'mzidentML' in outputs</filter> 320 <filter>'mzidentML' in outputs</filter>
307 </data> 321 </data>
308 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> 322 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
309 <filter>'cps' in outputs</filter> 323 <filter>'cps' in outputs</filter>
310 </data> 324 </data>
311 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> 325 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
312 <filter>'zip' in outputs</filter> 326 <filter>'zip' in outputs</filter>
313 </data> 327 </data>
400 </assert_contents> 414 </assert_contents>
401 </output> 415 </output>
402 <output name="output_proteins_phosphorylation"> 416 <output name="output_proteins_phosphorylation">
403 <assert_contents> 417 <assert_contents>
404 <has_text text="Phosphosite" /> 418 <has_text text="Phosphosite" />
419 <has_text text="cds.comp41779_c0_seq1" />
420 </assert_contents>
421 </output>
422 </test>
423 <test>
424 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
425 <param name="processing_options_selector" value="no"/>
426 <param name="filtering_options_selector" value="no"/>
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"/>
429 <output name="output_psm">
430 <assert_contents>
405 <has_text text="cds.comp41779_c0_seq1" /> 431 <has_text text="cds.comp41779_c0_seq1" />
406 </assert_contents> 432 </assert_contents>
407 </output> 433 </output>
408 </test> 434 </test>
409 </tests> 435 </tests>