Mercurial > repos > galaxyp > openms_mzmlsplitter

comparison MzMLSplitter.xml @ 12:095b7d42bfc2 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 19:14:47 +0000
parents 5aabc469cce0
children 609bc5efdcc9
comparison
equal deleted inserted replaced
11:ed505e649244 12:095b7d42bfc2
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="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Splits an mzML file into multiple parts</description> 5 <description>Splits an mzML file into multiple parts</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MzMLSplitter</token> 7 <token name="@EXECUTABLE@">MzMLSplitter</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@
38 <configfiles> 36 <configfiles>
39 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
40 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
41 </configfiles> 39 </configfiles>
42 <inputs> 40 <inputs>
43 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
44 <param name="parts" argument="-parts" type="integer" optional="true" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/> 42 <param argument="-parts" type="integer" optional="true" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
45 <param name="size" argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/> 43 <param argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
46 <param name="unit" argument="-unit" display="radio" type="select" optional="false" label="Unit for 'size' (base 1024)" help=""> 44 <param argument="-unit" type="select" optional="true" label="Unit for 'size' (base 1024)" help="">
47 <option value="KB">KB</option> 45 <option value="KB">KB</option>
48 <option value="MB" selected="true">MB</option> 46 <option value="MB" selected="true">MB</option>
49 <option value="GB">GB</option> 47 <option value="GB">GB</option>
50 <expand macro="list_string_san"/> 48 <expand macro="list_string_san" name="unit"/>
51 </param> 49 </param>
52 <param name="no_chrom" argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/> 50 <param argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/>
53 <param name="no_spec" argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/> 51 <param argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/>
54 <expand macro="adv_opts_macro"> 52 <expand macro="adv_opts_macro">
55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
57 <expand macro="list_string_san"/> 55 <expand macro="list_string_san" name="test"/>
58 </param> 56 </param>
59 </expand> 57 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
62 </param> 60 </param>
63 </inputs> 61 </inputs>
64 <outputs> 62 <outputs>
65 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> 63 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
66 <discover_datasets directory="out" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/> 64 <discover_datasets directory="out" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
67 </collection> 65 </collection>
68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
70 </data> 68 </data>
71 </outputs> 69 </outputs>
72 <tests> 70 <tests><!-- UTILS_MzMLSplitter_1 -->
73 <expand macro="autotest_MzMLSplitter"/> 71 <!-- UTILS_MzMLSplitter_2 -->
74 <expand macro="manutest_MzMLSplitter"/> 72 <test expect_num_outputs="2">
75 </tests> 73 <section name="adv_opts">
74 <param name="test" value="true"/>
75 </section>
76 <param name="in" value="FileFilter_1_input.mzML"/>
77 <param name="parts" value="2"/>
78 <param name="size" value="0"/>
79 <param name="unit" value="MB"/>
80 <param name="no_chrom" value="false"/>
81 <param name="no_spec" value="false"/>
82 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83 <output name="ctd_out" ftype="xml">
84 <assert_contents>
85 <is_valid_xml/>
86 </assert_contents>
87 </output>
88 <output_collection name="out" type="list" count="2">
89 <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
90 <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
91 </output_collection>
92 </test>
93 <test expect_num_outputs="2">
94 <section name="adv_opts">
95 <param name="test" value="true"/>
96 </section>
97 <param name="in" value="FileFilter_1_input.mzML"/>
98 <param name="parts" value="1"/>
99 <param name="size" value="40"/>
100 <param name="unit" value="KB"/>
101 <param name="no_chrom" value="false"/>
102 <param name="no_spec" value="false"/>
103 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
104 <output name="ctd_out" ftype="xml">
105 <assert_contents>
106 <is_valid_xml/>
107 </assert_contents>
108 </output>
109 <output_collection name="out" type="list" count="2">
110 <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
111 <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
112 </output_collection>
113 </test>
114 </tests>
76 <help><![CDATA[Splits an mzML file into multiple parts 115 <help><![CDATA[Splits an mzML file into multiple parts
77 116
78 117
79 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MzMLSplitter.html]]></help> 118 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MzMLSplitter.html]]></help>
80 <expand macro="references"/> 119 <expand macro="references"/>
81 </tool> 120 </tool>