Mercurial > repos > galaxyp > openms_sequencecoveragecalculator

comparison SequenceCoverageCalculator.xml @ 14:b5348eebc36c draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:39:10 +0000
parents 3fe59b1a1370
children
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13:3fe59b1a1370 14:b5348eebc36c
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Prints information about idXML files.</description> 4 <description>Prints information about idXML files</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">SequenceCoverageCalculator</token> 6 <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in_database && 16 mkdir in_database &&
18 ln -s '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' && 17 cp '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' &&
19 mkdir in_peptides && 18 mkdir in_peptides &&
20 ln -s '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' && 19 cp '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' &&
21 mkdir out && 20 mkdir out &&
22 21
23 ## Main program call 22 ## Main program call
24 23
25 set -o pipefail && 24 set -o pipefail &&
41 <configfiles> 40 <configfiles>
42 <inputs name="args_json" data_style="paths"/> 41 <inputs name="args_json" data_style="paths"/>
43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 </configfiles> 43 </configfiles>
45 <inputs> 44 <inputs>
46 <param argument="-in_database" type="data" format="fasta" optional="false" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/> 45 <param argument="-in_database" type="data" format="fasta" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/>
47 <param argument="-in_peptides" type="data" format="idxml" optional="false" label="input file containing the identified peptides" help=" select idxml data sets(s)"/> 46 <param argument="-in_peptides" type="data" format="idxml" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
48 <expand macro="adv_opts_macro"> 47 <expand macro="adv_opts_macro">
49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 48 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
50 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 49 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
51 <expand macro="list_string_san" name="test"/> 50 <expand macro="list_string_san" name="test"/>
52 </param> 51 </param>
53 </expand> 52 </expand>
54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 53 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 54 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
59 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/> 58 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 59 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 60 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
62 </data> 61 </data>
63 </outputs> 62 </outputs>
64 <tests><test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input --> 63 <tests>
65 <param name="adv_opts|test" value="true"/> 64 <test expect_num_outputs="1">
66 <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/> 65 <!-- took test data from another tool that also takes idXML and fasta as input -->
67 <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/> 66 <param name="adv_opts|test" value="true"/>
68 <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/> 67 <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
69 </test> 68 <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
70 </tests> 69 <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
70 </test>
71 </tests>
71 <help><![CDATA[Prints information about idXML files. 72 <help><![CDATA[Prints information about idXML files.
72 73
73 74
74 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SequenceCoverageCalculator.html]]></help> 75 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SequenceCoverageCalculator.html]]></help>
75 <expand macro="references"/> 76 <expand macro="references"/>
76 </tool> 77 </tool>