Mercurial > repos > galaxyp > openms_idextractor

comparison IDExtractor.xml @ 15:589bf635f424 draft

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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 19:07:40 +0000
parents 2a2fa2b57306
children a6124b08daff
comparison
equal deleted inserted replaced
14:ef4ecc9d45fb 15:589bf635f424
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="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description> 5 <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDExtractor</token> 7 <token name="@EXECUTABLE@">IDExtractor</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> 42 <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
45 <param name="number_of_peptides" argument="-number_of_peptides" type="integer" optional="true" min="1" value="10" label="Number of randomly chosen peptides" help=""/> 43 <param argument="-number_of_peptides" type="integer" optional="true" min="1" value="10" label="Number of randomly chosen peptides" help=""/>
46 <param name="number_of_rand_invokations" argument="-number_of_rand_invokations" type="integer" optional="true" min="0" value="0" label="Number of rand invocations before random draw" help=""/> 44 <param argument="-number_of_rand_invokations" type="integer" optional="true" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/>
47 <param name="best_hits" argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/> 45 <param argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/>
48 <expand macro="adv_opts_macro"> 46 <expand macro="adv_opts_macro">
49 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 47 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
50 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 48 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
51 <expand macro="list_string_san"/> 49 <expand macro="list_string_san" name="test"/>
52 </param> 50 </param>
53 </expand> 51 </expand>
54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 52 <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> 53 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
56 </param> 54 </param>
59 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 57 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
62 </data> 60 </data>
63 </outputs> 61 </outputs>
64 <tests> 62 <tests><test expect_num_outputs="1"><!-- -->
65 <expand macro="autotest_IDExtractor"/> 63 <param name="adv_opts|test" value="true"/>
66 <expand macro="manutest_IDExtractor"/> 64 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
67 </tests> 65 <param name="best_hits" value="true"/>
66 <param name="number_of_peptides" value="1"/>
67 <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
68 </test>
69 </tests>
68 <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files. 70 <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files.
69 71
70 72
71 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDExtractor.html]]></help> 73 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDExtractor.html]]></help>
72 <expand macro="references"/> 74 <expand macro="references"/>
73 </tool> 75 </tool>