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comparison IDExtractor.xml @ 12:4f72694caecd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:49:13 -0400
parents 7699f4110290
children 51bb6b5e73d3
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11:539a75dd888f 12:4f72694caecd
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="IDExtractor" name="IDExtractor" version="2.2.0"> 4 <tool id="IDExtractor" name="IDExtractor" version="2.3.0">
5 <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description> 5 <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDExtractor</token> 7 <token name="@EXECUTABLE@">IDExtractor</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>IDExtractor 13 <command detect_errors="aggressive"><![CDATA[IDExtractor
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
30 #if $adv_opts.adv_opts_selector=='advanced': 30 #if $adv_opts.adv_opts_selector=='advanced':
31 #if $adv_opts.param_force: 31 #if $adv_opts.param_force:
32 -force 32 -force
33 #end if 33 #end if
34 #end if 34 #end if
35 </command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> 37 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
38 <param name="param_number_of_peptides" type="integer" min="1" optional="True" value="10" label="Number of randomly chosen peptides" help="(-number_of_peptides) "/> 38 <param name="param_number_of_peptides" type="integer" min="1" optional="True" value="10" label="Number of randomly chosen peptides" help="(-number_of_peptides) "/>
39 <param name="param_number_of_rand_invokations" type="integer" min="0" optional="True" value="0" label="Number of rand invocations before random draw" help="(-number_of_rand_invokations) "/> 39 <param name="param_number_of_rand_invokations" type="integer" min="0" optional="True" value="0" label="Number of rand invocations before random draw" help="(-number_of_rand_invokations) "/>
40 <param name="param_best_hits" display="radio" type="boolean" truevalue="-best_hits" falsevalue="" checked="false" optional="True" label="If this flag is set the best n peptides are chosen" help="(-best_hits) "/> 40 <param name="param_best_hits" display="radio" type="boolean" truevalue="-best_hits" falsevalue="" checked="false" optional="True" label="If this flag is set the best n peptides are chosen" help="(-best_hits) "/>
46 <data name="param_out" format="idxml"/> 46 <data name="param_out" format="idxml"/>
47 </outputs> 47 </outputs>
48 <help>Extracts 'n' peptides randomly or best 'n' from idXML files. 48 <help>Extracts 'n' peptides randomly or best 'n' from idXML files.
49 49
50 50
51 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDExtractor.html</help> 51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDExtractor.html</help>
52 </tool> 52 </tool>