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comparison OpenSwathRewriteToFeatureXML.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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equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" 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>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token> 5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathRewriteToFeatureXML 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathRewriteToFeatureXML
11 14
12 -csv ${param_csv} 15 #if $param_csv:
13 -featureXML ${param_featureXML} 16 -csv $param_csv
14 -out ${param_out} 17 #end if
15 -FDR_cutoff ${param_FDR_cutoff} 18 #if $param_featureXML:
16 -threads \${GALAXY_SLOTS:-24} 19 -featureXML $param_featureXML
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_FDR_cutoff:
25 -FDR_cutoff $param_FDR_cutoff
26 #end if
27 -threads \${GALAXY_SLOTS:-24}
28 #if $adv_opts.adv_opts_selector=='advanced':
29 #if $adv_opts.param_force:
30 -force
31 #end if
32 #end if
17 </command> 33 </command>
18 <inputs> 34 <inputs>
19 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv)"/> 35 <param format="tabular" help="(-csv) " label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" name="param_csv" optional="True" type="data"/>
20 <param name="param_featureXML" type="data" format="featureXML" optional="False" label="input featureXML file" help="(-featureXML)"/> 36 <param format="xml" help="(-featureXML) " label="input featureXML file" name="param_featureXML" optional="False" type="data"/>
21 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" help="(-FDR_cutoff)"/> 37 <param help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" label="FDR cutoff (" name="param_FDR_cutoff" type="float" value="-1.0"/>
22 </inputs> 38 <expand macro="advanced_options">
23 <outputs> 39 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
24 <data name="param_out" label="output featureXML file" format="featureXML"/> 40 </expand>
25 </outputs> 41 </inputs>
26 <help>**What it does** 42 <outputs>
27 43 <data format="xml" name="param_out"/>
28 Combines featureXML and mProphet tsv to FDR filtered featureXML. 44 </outputs>
45 <help>Combines featureXML and mProphet tsv to FDR filtered featureXML.
29 46
30 47
31 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html 48 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html</help>
32 49 </tool>
33 @REFERENCES@
34 </help>
35 </tool>