Mercurial > repos > galaxyp > openms_openswathconfidencescoring

comparison OpenSwathConfidenceScoring.xml @ 12:eb25848baa9f 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 05:52:00 -0400
parents 7a2520759073
children 4b968ecbe77e
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11:3ad7260759bd 12:eb25848baa9f
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.2.0"> 4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.3.0">
5 <description>Compute confidence scores for OpenSwath results</description> 5 <description>Compute confidence scores for OpenSwath results</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token> 7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</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>OpenSwathConfidenceScoring 13 <command detect_errors="aggressive"><![CDATA[OpenSwathConfidenceScoring
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_lib: 18 #if $param_lib:
42 #end if 42 #end if
43 #if $adv_opts.param_GLM_dist_int: 43 #if $adv_opts.param_GLM_dist_int:
44 -GLM:dist_int $adv_opts.param_GLM_dist_int 44 -GLM:dist_int $adv_opts.param_GLM_dist_int
45 #end if 45 #end if
46 #end if 46 #end if
47 </command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file (OpenSwath results)" help="(-in) "/> 49 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file (OpenSwath results)" help="(-in) "/>
50 <param name="param_lib" type="data" format="traml" optional="False" label="Assay library" help="(-lib) "/> 50 <param name="param_lib" type="data" format="traml" optional="False" label="Assay library" help="(-lib) "/>
51 <param name="param_trafo" type="data" format="trafoxml" optional="True" label="Retention time transformation" help="(-trafo) "/> 51 <param name="param_trafo" type="data" format="trafoxml" optional="True" label="Retention time transformation" help="(-trafo) "/>
52 <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help="(-decoys) "/> 52 <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help="(-decoys) "/>
62 <data name="param_out" format="featurexml"/> 62 <data name="param_out" format="featurexml"/>
63 </outputs> 63 </outputs>
64 <help>Compute confidence scores for OpenSwath results 64 <help>Compute confidence scores for OpenSwath results
65 65
66 66
67 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html</help> 67 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathConfidenceScoring.html</help>
68 </tool> 68 </tool>