Mercurial > repos > galaxyp > openms_sequencecoveragecalculator

comparison SequenceCoverageCalculator.xml @ 7:e733f018e04c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:23:08 -0400
parents 81113c109ba1
children 01e5bd3ad317
comparison
equal deleted inserted replaced
6:1abbacf96b65 7:e733f018e04c
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 CTDConverter.--> 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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.3.0"> 4 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.3.0+galaxy1">
5 <description>Prints information about idXML files.</description> 5 <description>Prints information about idXML files.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SequenceCoverageCalculator</token> 7 <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="requirements"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <command detect_errors="aggressive"><![CDATA[SequenceCoverageCalculator
13 <command>SequenceCoverageCalculator
14
15 #if $param_in_database: 13 #if $param_in_database:
16 -in_database $param_in_database 14 -in_database '$param_in_database'
17 #end if 15 #end if
18 #if $param_in_peptides: 16 #if $param_in_peptides:
19 -in_peptides $param_in_peptides 17 -in_peptides '$param_in_peptides'
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if 18 #end if
24 #if $adv_opts.adv_opts_selector=='advanced': 19 #if $adv_opts.adv_opts_selector=='advanced':
25 #if $adv_opts.param_force: 20 #if $adv_opts.param_force:
26 -force 21 -force
27 #end if 22 #end if
28 #end if 23 #end if
29 </command> 24
25 ## fix output (https://github.com/OpenMS/OpenMS/issues/3605)
26 ## - add header
27 ## - remove reformat data
28 ## - remove summary info
29 ## - print summary info to stdout
30 | sed '1i#protein\tcoverage%\t#unique hits'
31 | sed 's/^\(.*\)(coverage%, #unique hits): \([0-9.]\+\)%, \([0-9]\+\)/\1\t\2\t\3/'
32 | tee tmpout
33 | egrep -v "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took" > '$param_out'
34 ##
35 && cat tmpout | egrep "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took"
36 ]]></command>
30 <inputs> 37 <inputs>
31 <param name="param_in_database" type="data" format="fasta" optional="False" label="input file containing the database in FASTA format" help="(-in_database) "/> 38 <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 name="param_in_peptides" type="data" format="idxml" optional="False" label="input file containing the identified peptides" help="(-in_peptides) "/> 39 <param name="param_in_peptides" type="data" format="idxml" optional="False" label="input file containing the identified peptides" help="(-in_peptides) "/>
33 <expand macro="advanced_options"> 40 <expand macro="advanced_options">
34 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 41 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
35 </expand> 42 </expand>
36 </inputs> 43 </inputs>
37 <outputs> 44 <outputs>
38 <data name="param_out" format="txt"/> 45 <data name="param_out" format="tabular"/>
39 </outputs> 46 </outputs>
47 <tests>
48 <test>
49 <param name="param_in_database" ftype="fasta" value="OpenPepXL_input.fasta"/>
50 <!-- generated with: IDFilter -best:strict -in ~/projects/OpenMS/src/tests/topp/OpenPepXL_output.idXML -out SequenceCoverageCalculator.idXML-->
51 <param name="param_in_peptides" ftype="idxml" value="SequenceCoverageCalculator.idXML" />
52 <output name="param_out" file="SequenceCoverageCalculator.tsv" ftype="tabular" />
53 </test>
54 </tests>
40 <help>Prints information about idXML files. 55 <help>Prints information about idXML files.
41 56
42 57
43 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html</help> 58 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SequenceCoverageCalculator.html</help>
59 <expand macro="references"/>
44 </tool> 60 </tool>