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comparison spectrast_create.xml @ 0:c8895a92b74d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/protk-galaxytools/tree/master/spectrast commit 34735d62618a252173e3c90436f240659484727a
author galaxyp
date Thu, 29 Mar 2018 09:51:50 -0400
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-1:000000000000 0:c8895a92b74d
1 <tool id="spectrast_create_1" name="SpectraST Create" version="5.0.0">
2 <description>Create Spectral Libraries</description>
3 <requirements>
4 <!--
5 <container type="docker">iracooke/protk-1.4.3</container>
6 -->
7 <requirement type="package" version="1.4.4a">protk</requirement>
8 <requirement type="package" version="5.0.0">tpp</requirement>
9 </requirements>
10 <stdio>
11 <exit_code range="1:" level="fatal" description="Job Failed" />
12 </stdio>
13 <command>
14 <![CDATA[
15 spectrast_create.rb --galaxy
16
17 #for $pepxml_file in $pepxml_files:
18 ${pepxml_file}
19 #end for
20
21 --spectrum-files='$spectrum_files'
22 --predicate 'Protein!~$decoy_prefix_string'
23 --p-thresh $p_thresh
24 --instrument-acquisition $instrument_acquisition
25 -o library
26
27 &&
28
29 mkdir -p $output.files_path
30
31 &&
32
33 cp library.splib library.spidx library.pepidx $output.files_path/
34
35 &&
36
37 echo "Spectral Library Primary File" > $output
38 ]]>
39 </command>
40 <inputs>
41
42 <param name="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
43 <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/>
44 <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/>
45 <param name="instrument_acquisition" type="text" value="CID-QTOF" label="Decoy String" size="20"
46 help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
47 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra."/>
48 <param name="p_thresh" type="float" value="0.99" min="0" max="1" label="Probability Threshold"
49 help="Matches scoring less than this value are discarded" />
50 </inputs>
51 <outputs>
52 <data format="splib" name="output"/>
53 </outputs>
54 <help>
55 <![CDATA[
56 **What it does**
57
58 Create Spectral Libraries.
59
60 ]]>
61 </help>
62 </tool>