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comparison MRMMapper.xml @ 14:47f82df5bdea 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 21:45:15 +0000
parents 9a6f6a0ed604
children
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13:9a6f6a0ed604 14:47f82df5bdea
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: [Targeted Experiments]--> 2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
4 <tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description> 4 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MRMMapper</token> 6 <token name="@EXECUTABLE@">MRMMapper</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($in.ext)' &&
19 mkdir tr && 18 mkdir tr &&
20 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && 19 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
21 mkdir out && 20 mkdir out &&
22 21
23 ## Main program call 22 ## Main program call
24 23
25 set -o pipefail && 24 set -o pipefail &&
41 <configfiles> 40 <configfiles>
42 <inputs name="args_json" data_style="paths"/> 41 <inputs name="args_json" data_style="paths"/>
43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 </configfiles> 43 </configfiles>
45 <inputs> 44 <inputs>
46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/> 45 <param argument="-in" type="data" format="mzml" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
47 <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/> 46 <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
48 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 47 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
49 <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" optional="true" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/> 48 <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
50 <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" optional="true" value="0.1" label="Product tolerance when mapping (in Th)" help=""/> 49 <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
51 <param name="map_multiple_assays" argument="-algorithm:map_multiple_assays" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output" help=""/> 50 <param name="map_multiple_assays" argument="-algorithm:map_multiple_assays" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output" help=""/>
52 <param name="error_on_unmapped" argument="-algorithm:error_on_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat remaining, unmapped chromatograms as an erro" help=""/> 51 <param name="error_on_unmapped" argument="-algorithm:error_on_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat remaining, unmapped chromatograms as an erro" help=""/>
53 </section> 52 </section>
54 <expand macro="adv_opts_macro"> 53 <expand macro="adv_opts_macro">
55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
56 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 55 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
57 <expand macro="list_string_san" name="test"/> 56 <expand macro="list_string_san" name="test"/>
58 </param> 57 </param>
59 </expand> 58 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 59 <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> 60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
66 <data name="ctd_out" format="xml" label="${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><!-- TOPP_MRMMapper_test_1 --> 69 <tests>
70 <!-- TOPP_MRMMapper_test_1 -->
71 <test expect_num_outputs="2"> 71 <test expect_num_outputs="2">
72 <section name="adv_opts"> 72 <section name="adv_opts">
73 <param name="force" value="false"/> 73 <param name="force" value="false"/>
74 <param name="test" value="true"/> 74 <param name="test" value="true"/>
75 </section> 75 </section>
76 <param name="in" value="MRMMapping_input.chrom.mzML"/> 76 <param name="in" value="MRMMapping_input.chrom.mzML"/>
77 <param name="tr" value="MRMMapping_input.TraML"/> 77 <param name="tr" value="MRMMapping_input.TraML"/>
78 <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 78 <output name="out" value="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
79 <section name="algorithm"> 79 <section name="algorithm">
80 <param name="precursor_tolerance" value="0.3"/> 80 <param name="precursor_tolerance" value="0.3"/>
81 <param name="product_tolerance" value="0.3"/> 81 <param name="product_tolerance" value="0.3"/>
82 <param name="map_multiple_assays" value="false"/> 82 <param name="map_multiple_assays" value="false"/>
83 <param name="error_on_unmapped" value="false"/> 83 <param name="error_on_unmapped" value="false"/>
86 <output name="ctd_out" ftype="xml"> 86 <output name="ctd_out" ftype="xml">
87 <assert_contents> 87 <assert_contents>
88 <is_valid_xml/> 88 <is_valid_xml/>
89 </assert_contents> 89 </assert_contents>
90 </output> 90 </output>
91 <assert_stdout>
92 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
93 </assert_stdout>
91 </test> 94 </test>
92 <!-- TOPP_MRMMapper_test_2 --> 95 <!-- TOPP_MRMMapper_test_2 -->
93 <test expect_num_outputs="2"> 96 <test expect_num_outputs="2">
94 <section name="adv_opts"> 97 <section name="adv_opts">
95 <param name="force" value="false"/> 98 <param name="force" value="false"/>
96 <param name="test" value="true"/> 99 <param name="test" value="true"/>
97 </section> 100 </section>
98 <param name="in" value="MRMMapping_input.chrom.mzML"/> 101 <param name="in" value="MRMMapping_input.chrom.mzML"/>
99 <param name="tr" value="MRMMapping_input_2.TraML"/> 102 <param name="tr" value="MRMMapping_input_2.TraML"/>
100 <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 103 <output name="out" value="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
101 <section name="algorithm"> 104 <section name="algorithm">
102 <param name="precursor_tolerance" value="0.01"/> 105 <param name="precursor_tolerance" value="0.01"/>
103 <param name="product_tolerance" value="0.01"/> 106 <param name="product_tolerance" value="0.01"/>
104 <param name="map_multiple_assays" value="false"/> 107 <param name="map_multiple_assays" value="false"/>
105 <param name="error_on_unmapped" value="false"/> 108 <param name="error_on_unmapped" value="false"/>
108 <output name="ctd_out" ftype="xml"> 111 <output name="ctd_out" ftype="xml">
109 <assert_contents> 112 <assert_contents>
110 <is_valid_xml/> 113 <is_valid_xml/>
111 </assert_contents> 114 </assert_contents>
112 </output> 115 </output>
116 <assert_stdout>
117 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
118 </assert_stdout>
113 </test> 119 </test>
114 </tests> 120 </tests>
115 <help><![CDATA[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) 121 <help><![CDATA[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
116 122
117 123
118 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MRMMapper.html]]></help> 124 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMMapper.html]]></help>
119 <expand macro="references"/> 125 <expand macro="references"/>
120 </tool> 126 </tool>