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comparison MzMLSplitter.xml @ 13:609bc5efdcc9 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 21:45:37 +0000
parents 095b7d42bfc2
children
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equal deleted inserted replaced
12:095b7d42bfc2 13:609bc5efdcc9
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: [File Filtering / Extraction / Merging]-->
4 <tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Splits an mzML file into multiple parts</description> 4 <description>Splits an mzML file into multiple parts</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MzMLSplitter</token> 6 <token name="@EXECUTABLE@">MzMLSplitter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
36 <configfiles> 35 <configfiles>
37 <inputs name="args_json" data_style="paths"/> 36 <inputs name="args_json" data_style="paths"/>
38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 37 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 </configfiles> 38 </configfiles>
40 <inputs> 39 <inputs>
41 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> 40 <param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/>
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=""/> 41 <param argument="-parts" type="integer" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
43 <param argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/> 42 <param argument="-size" type="integer" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
44 <param argument="-unit" type="select" optional="true" label="Unit for 'size' (base 1024)" help=""> 43 <param argument="-unit" type="select" label="Unit for 'size' (base 1024)" help="">
45 <option value="KB">KB</option> 44 <option value="KB">KB</option>
46 <option value="MB" selected="true">MB</option> 45 <option value="MB" selected="true">MB</option>
47 <option value="GB">GB</option> 46 <option value="GB">GB</option>
48 <expand macro="list_string_san" name="unit"/> 47 <expand macro="list_string_san" name="unit"/>
49 </param> 48 </param>
50 <param argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/> 49 <param argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/>
51 <param argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/> 50 <param argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/>
52 <expand macro="adv_opts_macro"> 51 <expand macro="adv_opts_macro">
53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 52 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 53 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
55 <expand macro="list_string_san" name="test"/> 54 <expand macro="list_string_san" name="test"/>
56 </param> 55 </param>
57 </expand> 56 </expand>
58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 </collection> 64 </collection>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data> 67 </data>
69 </outputs> 68 </outputs>
70 <tests><!-- UTILS_MzMLSplitter_1 --> 69 <tests>
71 <!-- UTILS_MzMLSplitter_2 --> 70 <!-- TOPP_MzMLSplitter_1 -->
72 <test expect_num_outputs="2"> 71 <!-- TOPP_MzMLSplitter_2 -->
73 <section name="adv_opts"> 72 <test expect_num_outputs="2">
74 <param name="test" value="true"/> 73 <section name="adv_opts">
75 </section> 74 <param name="test" value="true"/>
76 <param name="in" value="FileFilter_1_input.mzML"/> 75 </section>
77 <param name="parts" value="2"/> 76 <param name="in" value="FileFilter_1_input.mzML"/>
78 <param name="size" value="0"/> 77 <param name="parts" value="2"/>
79 <param name="unit" value="MB"/> 78 <param name="size" value="0"/>
80 <param name="no_chrom" value="false"/> 79 <param name="unit" value="MB"/>
81 <param name="no_spec" value="false"/> 80 <param name="no_chrom" value="false"/>
82 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 81 <param name="no_spec" value="false"/>
83 <output name="ctd_out" ftype="xml"> 82 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
84 <assert_contents> 83 <output name="ctd_out" ftype="xml">
85 <is_valid_xml/> 84 <assert_contents>
86 </assert_contents> 85 <is_valid_xml/>
87 </output> 86 </assert_contents>
88 <output_collection name="out" type="list" count="2"> 87 </output>
89 <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/> 88 <output_collection name="out" type="list" count="2">
90 <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/> 89 <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
91 </output_collection> 90 <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
92 </test> 91 </output_collection>
93 <test expect_num_outputs="2"> 92 </test>
94 <section name="adv_opts"> 93 <test expect_num_outputs="2">
95 <param name="test" value="true"/> 94 <section name="adv_opts">
96 </section> 95 <param name="test" value="true"/>
97 <param name="in" value="FileFilter_1_input.mzML"/> 96 </section>
98 <param name="parts" value="1"/> 97 <param name="in" value="FileFilter_1_input.mzML"/>
99 <param name="size" value="40"/> 98 <param name="parts" value="1"/>
100 <param name="unit" value="KB"/> 99 <param name="size" value="40"/>
101 <param name="no_chrom" value="false"/> 100 <param name="unit" value="KB"/>
102 <param name="no_spec" value="false"/> 101 <param name="no_chrom" value="false"/>
103 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 102 <param name="no_spec" value="false"/>
104 <output name="ctd_out" ftype="xml"> 103 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
105 <assert_contents> 104 <output name="ctd_out" ftype="xml">
106 <is_valid_xml/> 105 <assert_contents>
107 </assert_contents> 106 <is_valid_xml/>
108 </output> 107 </assert_contents>
109 <output_collection name="out" type="list" count="2"> 108 </output>
110 <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/> 109 <output_collection name="out" type="list" count="2">
111 <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/> 110 <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
112 </output_collection> 111 <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
113 </test> 112 </output_collection>
114 </tests> 113 </test>
114 </tests>
115 <help><![CDATA[Splits an mzML file into multiple parts 115 <help><![CDATA[Splits an mzML file into multiple parts
116 116
117 117
118 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MzMLSplitter.html]]></help> 118 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MzMLSplitter.html]]></help>
119 <expand macro="references"/> 119 <expand macro="references"/>
120 </tool> 120 </tool>