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comparison interprophet.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_interprophet_1" name="InterProphet" version="1.0.1"> 1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">galaxy_protk</requirement> 4 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
5 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> 5 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
6 </requirements> 6 </requirements>
7 7
8 8
9 <description>Combine Peptide Prophet results from multiple search engines</description> 9 <description>Combine Peptide Prophet results from multiple search engines</description>
10 10
11 <command interpreter="ruby"> 11 <command interpreter="bash">
12 12
13 interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob 13 interprophet_wrapper.sh
14 14
15 $output
16
17 $use_nss
18
19 $use_nrs
20
21 $use_nse
22
23 $use_nsi
24
25 $use_nsm
26
27 --minprob $minprob
15 28
16 ## Inputs. 29 ## Inputs.
17 ${first_input} 30 ${first_input}
18 #for $input_file in $input_files: 31 #for $input_file in $input_files:
19 ${input_file.additional_input} 32 ${input_file.additional_input}
27 40
28 <repeat name="input_files" title="Additional PepXML Input Files"> 41 <repeat name="input_files" title="Additional PepXML Input Files">
29 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/> 42 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
30 </repeat> 43 </repeat>
31 44
32 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/> 45 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--no-nss"/>
33 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/> 46 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--no-nrs"/>
34 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/> 47 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--no-nse"/>
35 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/> 48 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--no-nsi"/>
36 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/> 49 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--no-nsm"/>
37 50
38 <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/> 51 <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
39 52
40 </inputs> 53 </inputs>
41 <outputs> 54 <outputs>