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comparison peptide_prophet.xml @ 8:d19a95abf2e4

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Update
author Ira Cooke <iracooke@gmail.com>
date Sun, 09 Jun 2013 08:19:01 -0500
parents 3f0cb90824f1
children
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7:3f0cb90824f1 8:d19a95abf2e4
1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1"> 1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.2.0">galaxy_protk</requirement> 3 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
4 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> 4 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
5 </requirements> 5 </requirements>
6 6
7 <description>Calculate Peptide Prophet statistics on search results</description> 7 <description>Calculate Peptide Prophet statistics on search results</description>
8 8
9 <command interpreter="ruby">peptide_prophet_wrapper.rb ${output} ${input_file} -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi 9 <command interpreter="bash">
10 peptide_prophet_wrapper.sh $output $input_file
11
12 -r
13 $glyco
14 $useicat
15 $phospho
16 $usepi
17 $usert
18 $accurate_mass
19 $no_ntt
20 $no_nmc
21 $use_gamma
22 $use_only_expect
23 $force_fit
24 $allow_alt_instruments
25 $maldi
26
10 </command> 27 </command>
11 28
12 <inputs> 29 <inputs>
13 30
14 <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> 31 <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/>