Mercurial > repos > galaxyp > openms_sequencecoveragecalculator

comparison SequenceCoverageCalculator.xml @ 13:3fe59b1a1370 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:22:41 +0000
parents 7cfb36b97c87
children
comparison
equal deleted inserted replaced
12:452a5e307d05 13:3fe59b1a1370
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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
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)"/> 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)"/>
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)"/> 47 <param argument="-in_peptides" type="data" format="idxml" optional="false" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
50 <expand macro="adv_opts_macro"> 48 <expand macro="adv_opts_macro">
51 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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=""> 50 <param 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"/> 51 <expand macro="list_string_san" name="test"/>
54 </param> 52 </param>
55 </expand> 53 </expand>
56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
58 </param> 56 </param>
61 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/> 59 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
64 </data> 62 </data>
65 </outputs> 63 </outputs>
66 <tests> 64 <tests><test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input -->
67 <expand macro="autotest_SequenceCoverageCalculator"/> 65 <param name="adv_opts|test" value="true"/>
68 <expand macro="manutest_SequenceCoverageCalculator"/> 66 <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
69 </tests> 67 <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
68 <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
69 </test>
70 </tests>
70 <help><![CDATA[Prints information about idXML files. 71 <help><![CDATA[Prints information about idXML files.
71 72
72 73
73 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SequenceCoverageCalculator.html]]></help> 74 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SequenceCoverageCalculator.html]]></help>
74 <expand macro="references"/> 75 <expand macro="references"/>
75 </tool> 76 </tool>