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comparison IDMerger.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="IDMerger" name="IDMerger" version="1.12.0"> 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 <description>Merges several protein/peptide identification files into one file.</description> 3 <!--Proposed Tool Section: [File Handling]-->
4 <macros> 4 <tool id="IDMerger" name="IDMerger" version="2.0.0">
5 <token name="@EXECUTABLE@">IDMerger</token> 5 <description>Merges several protein/peptide identification files into one file.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">IDMerger</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>IDMerger 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDMerger
11 14
12 -in ${param_in} 15 -in
13 -out ${param_out} 16 $param_in1
14 -add_to ${param_add_to} 17 #for $infile in $inputs
15 ${param_annotate_file_origin} 18 $infile.param_in
16 ${param_pepxml_protxml} 19 #end for
17 -threads \${GALAXY_SLOTS:-24} 20 -out $param_out
21 #if $param_add_to:
22 -add_to $param_add_to
23 #end if
24 #if $param_annotate_file_origin:
25 -annotate_file_origin
26 #end if
27 #if $param_pepxml_protxml:
28 -pepxml_protxml
29 #end if
30 -threads \${GALAXY_SLOTS:-24}
31 #if $adv_opts.adv_opts_selector=='advanced':
32 #if $adv_opts.param_force:
33 -force
34 #end if
35 #end if
18 </command> 36 </command>
19 <inputs> 37 <inputs>
20 <param name="param_in" type="data" format="idXML" optional="False" size="20" label="Input files separated by blanks" help="(-in)"/> 38 <param name="param_in1" type="data" format="idxml" label="Input files" help="(-in)" />
21 <param name="param_add_to" type="data" format="idXML" optional="True" label="Optional input file. 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)." help="(-add_to)"/> 39 <repeat name="inputs" title="Input files">
22 <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin true" falsevalue="-annotate_file_origin false" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)." help="(-annotate_file_origin)"/> 40 <param name="param_in" type="data" format="idxml" label="Input files" help="(-in)" />
23 <param name="param_pepxml_protxml" type="boolean" truevalue="-pepxml_protxml true" falsevalue="-pepxml_protxml false" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file.#br#Exactly two input files are expected in this case. Not compatible with 'add_to'." help="(-pepxml_protxml)"/> 41 </repeat>
24 </inputs>
25 <outputs>
26 <data name="param_out" label="Output file" format="idXML"/>
27 </outputs>
28 <help>**What it does**
29 42
30 Merges several protein/peptide identification files into one file. 43 <param format="xml" 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)" label="Optional input file" name="param_add_to" optional="True" type="data"/>
44 <param checked="false" falsevalue="" help="(-annotate_file_origin) " label="Store the original filename in each protein/peptide identification (meta value: file_origin)" name="param_annotate_file_origin" optional="True" truevalue="-annotate_file_origin" type="boolean"/>
45 <param checked="false" falsevalue="" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'" label="Merge idXML files derived from a pepXML and corresponding protXML file" name="param_pepxml_protxml" optional="True" truevalue="-pepxml_protxml" type="boolean"/>
46 <expand macro="advanced_options">
47 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
48 </expand>
49 </inputs>
50 <outputs>
51 <data format="xml" name="param_out"/>
52 </outputs>
53 <help>Merges several protein/peptide identification files into one file.
31 54
32 55
33 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html 56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html</help>
34 57 </tool>
35 @REFERENCES@
36 </help>
37 </tool>