Mercurial > repos > galaxyp > openms_idmerger

comparison IDMerger.xml @ 0:75805008dd71 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 12:35:25 -0500
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children 8a47cd2b5b15
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-1:000000000000 0:75805008dd71
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: [File Handling]-->
4 <tool id="IDMerger" name="IDMerger" version="2.1.0">
5 <description>Merges several protein/peptide identification files into one file.</description>
6 <macros>
7 <token name="@EXECUTABLE@">IDMerger</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDMerger
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_out:
20 -out $param_out
21 #end if
22 #if $param_add_to:
23 -add_to $param_add_to
24 #end if
25 #if $param_annotate_file_origin:
26 -annotate_file_origin
27 #end if
28 #if $param_pepxml_protxml:
29 -pepxml_protxml
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="idxml" multiple="true" optional="False" size="30" label="Input files separated by blanks" 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_add_to" type="data" format="idxml" optional="True" label="Optional input file" help="(-add_to) IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)"/>
47 <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help="(-annotate_file_origin) "/>
48 <param name="param_pepxml_protxml" display="radio" type="boolean" truevalue="-pepxml_protxml" falsevalue="" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
49 <expand macro="advanced_options">
50 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
51 </expand>
52 </inputs>
53 <outputs>
54 <data name="param_out" format="idxml"/>
55 </outputs>
56 <help>Merges several protein/peptide identification files into one file.
57
58
59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html</help>
60 </tool>