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comparison SeedListGenerator.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
comparison
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="SeedListGenerator" name="SeedListGenerator" 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>Generates seed lists for feature detection.</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="SeedListGenerator" name="SeedListGenerator" version="2.0.0">
5 <token name="@EXECUTABLE@">SeedListGenerator</token> 5 <description>Generates seed lists for feature detection.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SeedListGenerator</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SeedListGenerator 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SeedListGenerator
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 ${param_use_peptide_mass} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18
19 #if $rep_param_out:
20 -out
21 #for token in $rep_param_out:
22 #if &quot; &quot; in str(token):
23 &quot;$token.param_out&quot;
24 #else
25 $token.param_out
26 #end if
27 #end for
28 #end if
29 #if $param_use_peptide_mass:
30 -use_peptide_mass
31 #end if
32 -threads \${GALAXY_SLOTS:-24}
33 #if $adv_opts.adv_opts_selector=='advanced':
34 #if $adv_opts.param_force:
35 -force
36 #end if
37 #end if
16 </command> 38 </command>
17 <inputs> 39 <inputs>
18 <param name="param_in" type="data" format="mzML,idXML,featureXML,consensusXML" optional="False" label="Input file (see below for details)" help="(-in)"/> 40 <param format="xml,consensusxml,mzml" help="(-in) " label="Input file (see below for details)" name="param_in" optional="False" type="data"/>
19 <param name="param_use_peptide_mass" type="boolean" truevalue="-use_peptide_mass true" falsevalue="-use_peptide_mass false" checked="false" optional="True" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help="(-use_peptide_mass)"/> 41 <param checked="false" falsevalue="" help="(-use_peptide_mass) " label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" name="param_use_peptide_mass" optional="True" truevalue="-use_peptide_mass" type="boolean"/>
20 </inputs> 42 <expand macro="advanced_options">
21 <outputs> 43 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
22 <data name="param_out" label="Output file(s)" format="featureXML"/> 44 </expand>
23 </outputs> 45 </inputs>
24 <help>**What it does** 46 <outputs>
25 47 <data format="xml" name="param_out"/>
26 Generates seed lists for feature detection. 48 </outputs>
49 <help>Generates seed lists for feature detection.
27 50
28 51
29 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html 52 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html</help>
30 53 </tool>
31 @REFERENCES@
32 </help>
33 </tool>