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comparison IDConflictResolver.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="IDConflictResolver" name="IDConflictResolver" 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>Resolves ambiguous annotations of features with peptide identifications</description> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <macros> 4 <tool id="IDConflictResolver" name="IDConflictResolver" version="2.0.0">
5 <token name="@EXECUTABLE@">IDConflictResolver</token> 5 <description>Resolves ambiguous annotations of features with peptide identifications</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">IDConflictResolver</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>IDConflictResolver 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDConflictResolver
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -threads \${GALAXY_SLOTS:-24} 17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 -threads \${GALAXY_SLOTS:-24}
22 #if $adv_opts.adv_opts_selector=='advanced':
23 #if $adv_opts.param_force:
24 -force
25 #end if
26 #end if
15 </command> 27 </command>
16 <inputs> 28 <inputs>
17 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="Input file (data annotated with identifications)" help="(-in)"/> 29 <param format="xml,consensusxml" help="(-in) " label="Input file (data annotated with identifications)" name="param_in" optional="False" type="data"/>
18 </inputs> 30 <expand macro="advanced_options">
19 <outputs> 31 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
20 <data name="param_out" label="Output file (data with one peptide identification per feature)" format="consensusXML"> 32 </expand>
21 <change_format> 33 </inputs>
22 <when input="param_out_type" value="featureXML" format="featureXML"/> 34 <outputs>
23 </change_format> 35 <data format="input" metadata_source="param_in" name="param_out"/>
24 </data> 36 </outputs>
25 </outputs> 37 <help>Resolves ambiguous annotations of features with peptide identifications
26 <help>**What it does**
27
28 Resolves ambiguous annotations of features with peptide identifications
29 38
30 39
31 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDConflictResolver.html 40 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDConflictResolver.html</help>
32 41 </tool>
33 @REFERENCES@
34 </help>
35 </tool>