Mercurial > repos > galaxyp > openms_openswathfilesplitter

comparison OpenSwathFileSplitter.xml @ 14:f8fcaa2dfd68 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 21:45:22 +0000
parents 4bb198c0bd3e
children
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equal deleted inserted replaced
13:4bb198c0bd3e 14:f8fcaa2dfd68
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="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Splits SWATH files into n files, each containing one window</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathFileSplitter</token> 6 <token name="@EXECUTABLE@">OpenSwathFileSplitter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
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($in.ext)' &&
19 mkdir outputDirectory && 18 mkdir outputDirectory &&
20 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 19 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
21 mkdir out_qc && 20 mkdir out_qc &&
22 #end if 21 #end if
23 22
49 <configfiles> 48 <configfiles>
50 <inputs name="args_json" data_style="paths"/> 49 <inputs name="args_json" data_style="paths"/>
51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
52 </configfiles> 51 </configfiles>
53 <inputs> 52 <inputs>
54 <param argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/> 53 <param argument="-in" type="data" format="mzml,mzxml" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
55 <expand macro="adv_opts_macro"> 54 <expand macro="adv_opts_macro">
56 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
57 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 56 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
58 <expand macro="list_string_san" name="test"/> 57 <expand macro="list_string_san" name="test"/>
59 </param> 58 </param>
60 </expand> 59 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
62 <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option> 61 <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option>
72 </data> 71 </data>
73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
75 </data> 74 </data>
76 </outputs> 75 </outputs>
77 <tests><!-- TOPP_OpenSwathFileSplitter_1 --> 76 <tests>
78 <test expect_num_outputs="3"> 77 <!-- TOPP_OpenSwathFileSplitter_1 -->
79 <section name="adv_opts"> 78 <test expect_num_outputs="3">
80 <param name="test" value="true"/> 79 <section name="adv_opts">
81 </section> 80 <param name="test" value="true"/>
82 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> 81 </section>
83 <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/> 82 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
84 <output_collection name="outputDirectory" count="6"> 83 <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
85 <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/> 84 <output_collection name="outputDirectory" count="6">
86 <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/> 85 <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
87 </output_collection> 86 <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
88 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> 87 </output_collection>
89 <output name="ctd_out" ftype="xml"> 88 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
90 <assert_contents> 89 <output name="ctd_out" ftype="xml">
91 <is_valid_xml/> 90 <assert_contents>
92 </assert_contents> 91 <is_valid_xml/>
93 </output> 92 </assert_contents>
94 </test> 93 </output>
95 </tests> 94 </test>
95 </tests>
96 <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.
97 97
98 98
99 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathFileSplitter.html]]></help> 99 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathFileSplitter.html]]></help>
100 <expand macro="references"/> 100 <expand macro="references"/>
101 </tool> 101 </tool>