Mercurial > repos > iracooke > spectrast

annotate spectrast_create.xml @ 6:2346c96c327e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Only fail on non-zero exit code
author iracooke
date Tue, 19 May 2015 20:01:34 -0400
parents d0a771b743ef
children c10b55821212
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
1 <tool id="spectrast_create_1" name="SpectraST Create" version="1.0.0">
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
2 <requirements>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
3 <container type="docker">iracooke/protk-1.4.2</container>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
4 <requirement type="package" version="1.4">protk</requirement>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
6 </requirements>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
7
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
8 <description>Create Spectral Libraries</description>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
9
6
2346c96c327e Only fail on non-zero exit code
iracooke
parents: 5
diff changeset
10 <stdio>
2346c96c327e Only fail on non-zero exit code
iracooke
parents: 5
diff changeset
11 <exit_code range="1:" level="fatal" description="Job Failed" />
2346c96c327e Only fail on non-zero exit code
iracooke
parents: 5
diff changeset
12 </stdio>
2346c96c327e Only fail on non-zero exit code
iracooke
parents: 5
diff changeset
13
0
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
14 <command>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
15 spectrast_create.rb --galaxy
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
16
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
17 #for $pepxml_file in $pepxml_files:
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
18 ${pepxml_file}
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
19 #end for
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
20
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
21 --spectrum-files='$spectrum_files'
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
22
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
23 --predicate 'Protein!~$decoy_prefix_string'
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
24
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
25 --p-thresh $p_thresh
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
26
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
27 --instrument-acquisition $instrument_acquisition
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
28
5
d0a771b743ef Fix output tag
iracooke
parents: 4
diff changeset
29 -o $output
0
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
30
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
31 </command>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
32
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
33 <inputs>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
34
1
9a717f816164 Fix input file types
iracooke
parents: 0
diff changeset
35 <param name="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
0
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
36
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
37 <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
38
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
39 <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
40
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
41 <param name="instrument_acquisition" help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
42 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra." type="text" value="CID-QTOF" label="Decoy String" size="20"/>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
43
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
44 <param name="p_thresh" help="Matches scoring less than this value are discarded" type="float" value="0.95" min="0" max="1" label="Probability Threshold"/>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
45
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
46
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
47 </inputs>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
48
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
49 <outputs>
4
d800158e1e91 Fix output tag
iracooke
parents: 3
diff changeset
50 <data format="splib" name="output"/>
0
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
51 </outputs>
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
52
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
53 </tool>