Mercurial > repos > galaxyp > openms_sequencecoveragecalculator

comparison SequenceCoverageCalculator.xml @ 12:31779bcc3991 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 23:13:48 +0000
parents 5adf97f241ef
children 6a658ff1be3f
comparison
equal deleted inserted replaced
11:5adf97f241ef 12:31779bcc3991
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+galaxy1"> 4 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="requirements"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <command detect_errors="aggressive"><![CDATA[SequenceCoverageCalculator 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 #if $param_in_database: 15 @EXT_FOO@
14 -in_database '$param_in_database' 16 #import re
15 #end if
16 #if $param_in_peptides:
17 -in_peptides '$param_in_peptides'
18 #end if
19 #if $adv_opts.adv_opts_selector=='advanced':
20 #if $adv_opts.param_force:
21 -force
22 #end if
23 #end if
24 17
25 ## fix output (https://github.com/OpenMS/OpenMS/issues/3605) 18 ## Preprocessing
26 ## - add header 19 mkdir in_database &&
27 ## - remove reformat data 20 ln -s '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' &&
28 ## - remove summary info 21 mkdir in_peptides &&
29 ## - print summary info to stdout 22 ln -s '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' &&
30 | sed '1i#protein\tcoverage%\t#unique hits' 23 mkdir out &&
31 | sed 's/^\(.*\)(coverage%, #unique hits): \([0-9.]\+\)%, \([0-9]\+\)/\1\t\2\t\3/' 24
32 | tee tmpout 25 ## Main program call
33 | egrep -v "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took" > '$param_out' 26
34 ## 27 set -o pipefail &&
35 && cat tmpout | egrep "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took" 28 @EXECUTABLE@ -write_ctd ./ &&
36 ]]></command> 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 -in_database
32 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)'
33 -in_peptides
34 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)'
35 -out
36 'out/output.${gxy2omsext("txt")}'
37
38 ## Postprocessing
39 && mv 'out/output.${gxy2omsext("txt")}' '$out'
40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command>
43 <configfiles>
44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles>
37 <inputs> 47 <inputs>
38 <param name="param_in_database" type="data" format="fasta" optional="False" label="input file containing the database in FASTA format" help="(-in_database) "/> 48 <param name="in_database" argument="-in_database" type="data" format="fasta" optional="false" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/>
39 <param name="param_in_peptides" type="data" format="idxml" optional="False" label="input file containing the identified peptides" help="(-in_peptides) "/> 49 <param name="in_peptides" argument="-in_peptides" type="data" format="idxml" optional="false" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
40 <expand macro="advanced_options"> 50 <expand macro="adv_opts_macro">
41 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 51 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
52 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
53 <expand macro="list_string_san"/>
54 </param>
42 </expand> 55 </expand>
56 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
58 </param>
43 </inputs> 59 </inputs>
44 <outputs> 60 <outputs>
45 <data name="param_out" format="tabular"/> 61 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
64 </data>
46 </outputs> 65 </outputs>
47 <tests> 66 <tests>
48 <test> 67 <expand macro="autotest_SequenceCoverageCalculator"/>
49 <param name="param_in_database" ftype="fasta" value="OpenPepXL_input.fasta"/> 68 <expand macro="manutest_SequenceCoverageCalculator"/>
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> 69 </tests>
55 <help>Prints information about idXML files. 70 <help><![CDATA[Prints information about idXML files.
56 71
57 72
58 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SequenceCoverageCalculator.html</help> 73 For more information, visit http://www.openms.de/documentation/UTILS_SequenceCoverageCalculator.html]]></help>
59 <expand macro="references"/> 74 <expand macro="references"/>
60 </tool> 75 </tool>