Mercurial > repos > galaxyp > openms_openswathfilesplitter

comparison OpenSwathFileSplitter.xml @ 13:4bb198c0bd3e 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 19:02:09 +0000
parents 40abe25cb21c
children f8fcaa2dfd68
comparison
equal deleted inserted replaced
12:89254095cbf6 13:4bb198c0bd3e
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Splits SWATH files into n files, each containing one window.</description> 5 <description>Splits SWATH files into n files, each containing one window.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathFileSplitter</token> 7 <token name="@EXECUTABLE@">OpenSwathFileSplitter</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@
51 <configfiles> 49 <configfiles>
52 <inputs name="args_json" data_style="paths"/> 50 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles> 52 </configfiles>
55 <inputs> 53 <inputs>
56 <param name="in" argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/> 54 <param argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
57 <expand macro="adv_opts_macro"> 55 <expand macro="adv_opts_macro">
58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 56 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 57 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
60 <expand macro="list_string_san"/> 58 <expand macro="list_string_san" name="test"/>
61 </param> 59 </param>
62 </expand> 60 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
64 <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option> 62 <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option>
65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
66 </param> 64 </param>
67 </inputs> 65 </inputs>
68 <outputs> 66 <outputs>
69 <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory"> 67 <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
70 <discover_datasets directory="outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/> 68 <discover_datasets directory="outputDirectory" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
71 </collection> 69 </collection>
72 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json"> 70 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
73 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter> 71 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
74 </data> 72 </data>
75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
77 </data> 75 </data>
78 </outputs> 76 </outputs>
79 <tests> 77 <tests><!-- TOPP_OpenSwathFileSplitter_1 -->
80 <expand macro="autotest_OpenSwathFileSplitter"/> 78 <test expect_num_outputs="3">
81 <expand macro="manutest_OpenSwathFileSplitter"/> 79 <section name="adv_opts">
82 </tests> 80 <param name="test" value="true"/>
81 </section>
82 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
83 <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
84 <output_collection name="outputDirectory" count="6">
85 <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
86 <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
87 </output_collection>
88 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
89 <output name="ctd_out" ftype="xml">
90 <assert_contents>
91 <is_valid_xml/>
92 </assert_contents>
93 </output>
94 </test>
95 </tests>
83 <help><![CDATA[Splits SWATH files into n files, each containing one window. 96 <help><![CDATA[Splits SWATH files into n files, each containing one window.
84 97
85 98
86 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathFileSplitter.html]]></help> 99 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathFileSplitter.html]]></help>
87 <expand macro="references"/> 100 <expand macro="references"/>
88 </tool> 101 </tool>