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comparison OpenSwathFeatureXMLToTSV.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="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" 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>Converts a featureXML to a mProphet tsv.</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token> 5 <description>Converts a featureXML to a mProphet tsv.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathFeatureXMLToTSV 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathFeatureXMLToTSV
11 14
12 -in ${param_in} 15 -in
13 -tr ${param_tr} 16 #for token in $param_in:
14 -out ${param_out} 17 $token
15 ${param_short_format} 18 #end for
16 -best_scoring_peptide ${param_best_scoring_peptide} 19 #if $param_tr:
17 -threads \${GALAXY_SLOTS:-24} 20 -tr $param_tr
21 #end if
22 #if $param_out:
23 -out $param_out
24 #end if
25 #if $param_short_format:
26 -short_format
27 #end if
28 #if $param_best_scoring_peptide:
29 -best_scoring_peptide &quot;$param_best_scoring_peptide&quot;
30 #end if
31 -threads \${GALAXY_SLOTS:-24}
32 #if $adv_opts.adv_opts_selector=='advanced':
33 #if $adv_opts.param_force:
34 -force
35 #end if
36 #end if
18 </command> 37 </command>
19 <inputs> 38 <inputs>
20 <param name="param_in" type="data" format="featureXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/> 39 <param format="xml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
21 <param name="param_tr" type="data" format="" optional="False" label="TraML transition file" help="(-tr)"/> 40 <sanitizer>
22 <param name="param_short_format" type="boolean" truevalue="-short_format true" falsevalue="-short_format false" checked="false" optional="True" label="Whether to write short (one peptide per line) or long format (one transition per line)." help="(-short_format)"/> 41 <valid initial="string.printable">
23 <param name="param_best_scoring_peptide" type="text" size="20" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide)"/> 42 <remove value="'"/>
24 </inputs> 43 <remove value="&quot;"/>
25 <outputs> 44 </valid>
26 <data name="param_out" label="tsv output file (mProphet compatible)" format="tabular"/> 45 </sanitizer>
27 </outputs> 46 </param>
28 <help>**What it does** 47 <param format="traml" help="(-tr) " label="TraML transition file" name="param_tr" optional="False" type="data"/>
29 48 <param checked="false" falsevalue="" help="(-short_format) " label="Whether to write short (one peptide per line) or long format (one transition per line)" name="param_short_format" optional="True" truevalue="-short_format" type="boolean"/>
30 Converts a featureXML to a mProphet tsv. 49 <param help="(-best_scoring_peptide) " label="If only the best scoring feature per peptide should be printed, give the variable name" name="param_best_scoring_peptide" size="30" type="text">
50 <sanitizer>
51 <valid initial="string.printable">
52 <remove value="'"/>
53 <remove value="&quot;"/>
54 </valid>
55 </sanitizer>
56 </param>
57 <expand macro="advanced_options">
58 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
59 </expand>
60 </inputs>
61 <outputs>
62 <data format="tabular" name="param_out"/>
63 </outputs>
64 <help>Converts a featureXML to a mProphet tsv.
31 65
32 66
33 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html 67 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
34 68 </tool>
35 @REFERENCES@
36 </help>
37 </tool>