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comparison IDRipper.xml @ 14:e64214bd2f6e 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 21:45:30 +0000
parents 7960e660446e
children
comparison
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13:7960e660446e 14:e64214bd2f6e
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: [File Handling]--> 2 <!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
4 <tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Split protein/peptide identification file into several files according to identification run and annotated file origin.</description> 4 <description>Split protein/peptide identification file into several files according to identification run and annotated file origin</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDRipper</token> 6 <token name="@EXECUTABLE@">IDRipper</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 && 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="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/> 40 <param argument="-in" type="data" format="idxml" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
42 <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/> 41 <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/>
43 <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" help=""/> 42 <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" help=""/>
44 <expand macro="adv_opts_macro"> 43 <expand macro="adv_opts_macro">
45 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 44 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
46 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 45 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
47 <expand macro="list_string_san" name="test"/> 46 <expand macro="list_string_san" name="test"/>
48 </param> 47 </param>
49 </expand> 48 </expand>
50 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 49 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
51 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 50 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
57 </collection> 56 </collection>
58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
60 </data> 59 </data>
61 </outputs> 60 </outputs>
62 <tests><!-- TOPP_IDRipper_1 --> 61 <tests>
62 <!-- TOPP_IDRipper_1 -->
63 <!-- TOPP_IDRipper_2 --> 63 <!-- TOPP_IDRipper_2 -->
64 <!-- TOPP_IDRipper_2a --> 64 <!-- TOPP_IDRipper_2a -->
65 <!-- TOPP_IDRipper_3 --> 65 <!-- TOPP_IDRipper_3 -->
66 <test expect_num_outputs="2"> 66 <test expect_num_outputs="2">
67 <section name="adv_opts"> 67 <section name="adv_opts">
68 <param name="test" value="true"/> 68 <param name="test" value="true"/>
69 </section> 69 </section>
70 <param name="in" value="IDRipper_1_input.idXML"/> 70 <param name="in" value="IDRipper_1_input.idXML"/>
71 <output_collection name="out" count="2"> 71 <output_collection name="out" count="2">
78 <output name="ctd_out" ftype="xml"> 78 <output name="ctd_out" ftype="xml">
79 <assert_contents> 79 <assert_contents>
80 <is_valid_xml/> 80 <is_valid_xml/>
81 </assert_contents> 81 </assert_contents>
82 </output> 82 </output>
83 </test><test expect_num_outputs="2"> 83 </test>
84 <test expect_num_outputs="2">
84 <section name="adv_opts"> 85 <section name="adv_opts">
85 <param name="test" value="true"/> 86 <param name="test" value="true"/>
86 </section> 87 </section>
87 <param name="in" value="IDRipper_2_input.idXML"/> 88 <param name="in" value="IDRipper_2_input.idXML"/>
88 <output_collection name="out" count="3"> 89 <output_collection name="out" count="3">
96 <output name="ctd_out" ftype="xml"> 97 <output name="ctd_out" ftype="xml">
97 <assert_contents> 98 <assert_contents>
98 <is_valid_xml/> 99 <is_valid_xml/>
99 </assert_contents> 100 </assert_contents>
100 </output> 101 </output>
101 </test><test expect_num_outputs="2"> 102 </test>
103 <test expect_num_outputs="2">
102 <section name="adv_opts"> 104 <section name="adv_opts">
103 <param name="test" value="true"/> 105 <param name="test" value="true"/>
104 </section> 106 </section>
105 <param name="in" value="IDRipper_2_input.idXML"/> 107 <param name="in" value="IDRipper_2_input.idXML"/>
106 <output_collection name="out" count="2"> 108 <output_collection name="out" count="2">
113 <output name="ctd_out" ftype="xml"> 115 <output name="ctd_out" ftype="xml">
114 <assert_contents> 116 <assert_contents>
115 <is_valid_xml/> 117 <is_valid_xml/>
116 </assert_contents> 118 </assert_contents>
117 </output> 119 </output>
118 </test><test expect_num_outputs="2"> 120 </test>
121 <test expect_num_outputs="2">
119 <section name="adv_opts"> 122 <section name="adv_opts">
120 <param name="test" value="true"/> 123 <param name="test" value="true"/>
121 </section> 124 </section>
122 <param name="in" value="IDRipper_3_output.idXML"/> 125 <param name="in" value="IDRipper_3_output.idXML"/>
123 <output_collection name="out" count="2"> 126 <output_collection name="out" count="2">
131 <assert_contents> 134 <assert_contents>
132 <is_valid_xml/> 135 <is_valid_xml/>
133 </assert_contents> 136 </assert_contents>
134 </output> 137 </output>
135 </test> 138 </test>
136 </tests> 139 </tests>
137 <help><![CDATA[Split protein/peptide identification file into several files according to identification run and annotated file origin. 140 <help><![CDATA[Split protein/peptide identification file into several files according to identification run and annotated file origin.
138 141
139 142
140 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRipper.html]]></help> 143 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDRipper.html]]></help>
141 <expand macro="references"/> 144 <expand macro="references"/>
142 </tool> 145 </tool>