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comparison ConvertTSVToTraML.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="ConvertTSVToTraML" name="ConvertTSVToTraML" version="2.0.0">
3 <description>Converts an OpenSWATH transition TSV file to a TraML file</description>
4 <macros>
5 <token name="@EXECUTABLE@">ConvertTSVToTraML</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>ConvertTSVToTraML
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 -threads \${GALAXY_SLOTS:-24}
19 #if $adv_opts.adv_opts_selector=='advanced':
20 #if $adv_opts.param_force:
21 -force
22 #end if
23 #if $adv_opts.param_algorithm_retentionTimeInterpretation:
24 -algorithm:retentionTimeInterpretation
25 #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation):
26 "$adv_opts.param_algorithm_retentionTimeInterpretation"
27 #else
28 $adv_opts.param_algorithm_retentionTimeInterpretation
29 #end if
30 #end if
31 #if $adv_opts.param_algorithm_override_group_label_check:
32 -algorithm:override_group_label_check
33 #end if
34 #end if
35 </command>
36 <inputs>
37 <param name="param_in" type="data" format="tabular" optional="False" label="Input OpenSWATH transition TSV file or SpectraST MRM file" help="(-in) &lt;br&gt; See http://www.openms.de/current_doxygen/html/UTILS_ConvertTSVToTraML.html for format"/>
38 <expand macro="advanced_options">
39 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
40 <param name="param_algorithm_retentionTimeInterpretation" type="select" optional="True" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) ">
41 <option value="iRT">iRT</option>
42 <option value="seconds">seconds</option>
43 <option value="minutes">minutes</option>
44 </param>
45 <param name="param_algorithm_override_group_label_check" type="boolean" truevalue="-algorithm:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
46 </expand>
47 </inputs>
48 <outputs>
49 <data name="param_out" format="traml"/>
50 </outputs>
51 <help>**What it does**
52
53 Converts an OpenSWATH transition TSV file to a TraML file
54
55
56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConvertTSVToTraML.html</help>
57 <expand macro="references"/>
58 </tool>