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comparison OpenSwathFeatureXMLToTSV.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.0.0">
3 <description>Converts a featureXML to a mProphet tsv.</description>
4 <macros>
5 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>OpenSwathFeatureXMLToTSV
11
12 -in
13 #for token in $param_in:
14 $token
15 #end for
16 #if $param_tr:
17 -tr $param_tr
18 #end if
19 #if $param_out:
20 -out $param_out
21 #end if
22 #if $param_short_format:
23 -short_format
24 #end if
25 #if $param_best_scoring_peptide:
26 -best_scoring_peptide "$param_best_scoring_peptide"
27 #end if
28 -threads \${GALAXY_SLOTS:-24}
29 #if $adv_opts.adv_opts_selector=='advanced':
30 #if $adv_opts.param_force:
31 -force
32 #end if
33 #end if
34 </command>
35 <inputs>
36 <param name="param_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
37 <sanitizer>
38 <valid initial="string.printable">
39 <remove value="'"/>
40 <remove value="&quot;"/>
41 </valid>
42 </sanitizer>
43 </param>
44 <param name="param_tr" type="data" format="traml" optional="False" label="TraML transition file" help="(-tr) "/>
45 <param name="param_short_format" 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) "/>
46 <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) ">
47 <sanitizer>
48 <valid initial="string.printable">
49 <remove value="'"/>
50 <remove value="&quot;"/>
51 </valid>
52 </sanitizer>
53 </param>
54 <expand macro="advanced_options">
55 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
56 </expand>
57 </inputs>
58 <outputs>
59 <data name="param_out" format="tabular"/>
60 </outputs>
61 <help>**What it does**
62
63 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 <expand macro="references"/>
68 </tool>