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comparison SequenceCoverageCalculator.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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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" 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>Prints information about idXML files.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.0.0">
5 <token name="@EXECUTABLE@">SequenceCoverageCalculator</token> 5 <description>Prints information about idXML files.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SequenceCoverageCalculator 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SequenceCoverageCalculator
11 14
12 -in_database ${param_in_database} 15 #if $param_in_database:
13 -in_peptides ${param_in_peptides} 16 -in_database $param_in_database
14 -out ${param_out} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_in_peptides:
19 -in_peptides $param_in_peptides
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
25 #if $adv_opts.adv_opts_selector=='advanced':
26 #if $adv_opts.param_force:
27 -force
28 #end if
29 #end if
16 </command> 30 </command>
17 <inputs> 31 <inputs>
18 <param name="param_in_database" type="data" format="fasta" optional="False" label="input file containing the database in FASTA format" help="(-in_database)"/> 32 <param format="fasta" help="(-in_database) " label="input file containing the database in FASTA format" name="param_in_database" optional="False" type="data"/>
19 <param name="param_in_peptides" type="data" format="idXML" optional="False" label="input file containing the identified peptides" help="(-in_peptides)"/> 33 <param format="xml" help="(-in_peptides) " label="input file containing the identified peptides" name="param_in_peptides" optional="False" type="data"/>
20 </inputs> 34 <expand macro="advanced_options">
21 <outputs> 35 <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="Optional text output file. If left out, the output is written to the command line." format="txt"/> 36 </expand>
23 </outputs> 37 </inputs>
24 <help>**What it does** 38 <outputs>
25 39 <data format="txt" name="param_out"/>
26 Prints information about idXML files. 40 </outputs>
41 <help>Prints information about idXML files.
27 42
28 43
29 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html 44 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html</help>
30 45 </tool>
31 @REFERENCES@
32 </help>
33 </tool>