Mercurial > repos > galaxyp > openms_seedlistgenerator

comparison SeedListGenerator.xml @ 8:f6076d07a33a 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 21:39:33 +0000
parents f3c72f54b9eb
children
comparison
equal deleted inserted replaced
7:f3c72f54b9eb 8:f6076d07a33a
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: [Quantitation]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Generates seed lists for feature detection.</description> 4 <description>Generates seed lists for feature detection</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">SeedListGenerator</token> 6 <token name="@EXECUTABLE@">SeedListGenerator</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 out_prefix && 18 mkdir out_prefix &&
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="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/> 40 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file (see below for details)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
42 <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/> 41 <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
43 <expand macro="adv_opts_macro"> 42 <expand macro="adv_opts_macro">
44 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 43 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
45 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 44 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
46 <expand macro="list_string_san" name="test"/> 45 <expand macro="list_string_san" name="test"/>
47 </param> 46 </param>
48 </expand> 47 </expand>
49 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 48 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
50 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 49 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
56 </collection> 55 </collection>
57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 56 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 57 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
59 </data> 58 </data>
60 </outputs> 59 </outputs>
61 <tests><!-- TOPP_SeedListGenerator_1 --> 60 <tests>
61 <!-- TOPP_SeedListGenerator_1 -->
62 <!-- TOPP_SeedListGenerator_2 --> 62 <!-- TOPP_SeedListGenerator_2 -->
63 <!-- TOPP_SeedListGenerator_3 --> 63 <!-- TOPP_SeedListGenerator_3 -->
64 <test expect_num_outputs="2"> 64 <test expect_num_outputs="2">
65 <section name="adv_opts"> 65 <section name="adv_opts">
66 <param name="test" value="true"/> 66 <param name="test" value="true"/>
67 </section> 67 </section>
68 <param name="in" value="PepXMLFile_test.mzML"/> 68 <param name="in" value="PepXMLFile_test.mzML"/>
69 <output_collection name="out_prefix" count="1"> 69 <output_collection name="out_prefix" count="1">
74 <output name="ctd_out" ftype="xml"> 74 <output name="ctd_out" ftype="xml">
75 <assert_contents> 75 <assert_contents>
76 <is_valid_xml/> 76 <is_valid_xml/>
77 </assert_contents> 77 </assert_contents>
78 </output> 78 </output>
79 </test><test expect_num_outputs="2"> 79 </test>
80 <test expect_num_outputs="2">
80 <section name="adv_opts"> 81 <section name="adv_opts">
81 <param name="test" value="true"/> 82 <param name="test" value="true"/>
82 </section> 83 </section>
83 <param name="in" value="IDMapper_1_output.featureXML"/> 84 <param name="in" value="IDMapper_1_output.featureXML"/>
84 <output_collection name="out_prefix" count="1"> 85 <output_collection name="out_prefix" count="1">
89 <output name="ctd_out" ftype="xml"> 90 <output name="ctd_out" ftype="xml">
90 <assert_contents> 91 <assert_contents>
91 <is_valid_xml/> 92 <is_valid_xml/>
92 </assert_contents> 93 </assert_contents>
93 </output> 94 </output>
94 </test><test expect_num_outputs="2"> 95 </test>
96 <test expect_num_outputs="2">
95 <section name="adv_opts"> 97 <section name="adv_opts">
96 <param name="test" value="true"/> 98 <param name="test" value="true"/>
97 </section> 99 </section>
98 <param name="in" value="ConsensusXMLFile_1.consensusXML"/> 100 <param name="in" value="ConsensusXMLFile_1.consensusXML"/>
99 <output_collection name="out_prefix" count="2"> 101 <output_collection name="out_prefix" count="2">
106 <assert_contents> 108 <assert_contents>
107 <is_valid_xml/> 109 <is_valid_xml/>
108 </assert_contents> 110 </assert_contents>
109 </output> 111 </output>
110 </test> 112 </test>
111 </tests> 113 </tests>
112 <help><![CDATA[Generates seed lists for feature detection. 114 <help><![CDATA[Generates seed lists for feature detection.
113 115
114 116
115 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SeedListGenerator.html]]></help> 117 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SeedListGenerator.html]]></help>
116 <expand macro="references"/> 118 <expand macro="references"/>
117 </tool> 119 </tool>