Mercurial > repos > iracooke > tpp_prophets

comparison protein_prophet.xml @ 8:d19a95abf2e4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update
author Ira Cooke <iracooke@gmail.com>
date Sun, 09 Jun 2013 08:19:01 -0500
parents 3f0cb90824f1
children
comparison
equal deleted inserted replaced
7:3f0cb90824f1 8:d19a95abf2e4
1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1"> 1 <tool id="proteomics_search_protein_prophet_1" name="Protein 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 Protein Prophet statistics on search results</description> 7 <description>Calculate Protein Prophet statistics on search results</description>
8 8
9 9
10 <!-- Note .. the input file is assumed to be the first argument --> 10 <!-- Note .. the input file is assumed to be the first argument -->
11 <command interpreter="ruby">protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command> 11 <command interpreter="bash">
12 protein_prophet_wrapper.sh
13
14 --galaxy $input_file
15
16 -r
17
18 $iproph
19 $nooccam
20 $groupwts
21 $normprotlen
22 $logprobs
23 $confem
24 $allpeps
25 $unmapped
26 $instances
27 $delude
28
29 --minprob=$minprob
30 --minindep=$minindep
31 </command>
12 <inputs> 32 <inputs>
13 33
14 <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> 34 <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>
15 35
16 36