Mercurial > repos > galaxyp > openms_openswathfeaturexmltotsv

comparison OpenSwathFeatureXMLToTSV.xml @ 0:c1f46b63e8c8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:19:02 -0500
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-1:000000000000 0:c1f46b63e8c8
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.1.0">
5 <description>Converts a featureXML to a mProphet tsv.</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathFeatureXMLToTSV
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_tr:
20 -tr $param_tr
21 #end if
22 #if $param_out:
23 -out $param_out
24 #end if
25 #if $param_short_format:
26 -short_format
27 #end if
28 #if $param_best_scoring_peptide:
29 -best_scoring_peptide "$param_best_scoring_peptide"
30 #end if
31 #if $adv_opts.adv_opts_selector=='advanced':
32 #if $adv_opts.param_force:
33 -force
34 #end if
35 #end if
36 </command>
37 <inputs>
38 <param name="param_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
39 <sanitizer>
40 <valid initial="string.printable">
41 <remove value="'"/>
42 <remove value="&quot;"/>
43 </valid>
44 </sanitizer>
45 </param>
46 <param name="param_tr" type="data" format="traml" optional="False" label="TraML transition file" help="(-tr) "/>
47 <param name="param_short_format" display="radio" type="boolean" truevalue="-short_format" falsevalue="" checked="false" optional="True" label="Whether to write short (one peptide per line) or long format (one transition per line)" help="(-short_format) "/>
48 <param name="param_best_scoring_peptide" type="text" size="30" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide) ">
49 <sanitizer>
50 <valid initial="string.printable">
51 <remove value="'"/>
52 <remove value="&quot;"/>
53 </valid>
54 </sanitizer>
55 </param>
56 <expand macro="advanced_options">
57 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
58 </expand>
59 </inputs>
60 <outputs>
61 <data name="param_out" format="tabular"/>
62 </outputs>
63 <help>Converts a featureXML to a mProphet tsv.
64
65
66 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
67 </tool>