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comparison DTAExtractor.xml @ 18:78024781d209 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 21:43:05 +0000
parents 79706b7647c3
children
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17:79706b7647c3 18:78024781d209
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="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Extracts spectra of an MS run file to several files in DTA format.</description> 4 <description>Extracts spectra of an MS run file to several files in DTA format</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">DTAExtractor</token> 6 <token name="@EXECUTABLE@">DTAExtractor</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 18
20 ## Main program call 19 ## Main program call
21 20
22 set -o pipefail && 21 set -o pipefail &&
23 @EXECUTABLE@ -write_ctd ./ && 22 @EXECUTABLE@ -write_ctd ./ &&
34 <configfiles> 33 <configfiles>
35 <inputs name="args_json" data_style="paths"/> 34 <inputs name="args_json" data_style="paths"/>
36 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 35 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
37 </configfiles> 36 </configfiles>
38 <inputs> 37 <inputs>
39 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 38 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
40 <param argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help=""> 39 <param argument="-out" type="text" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
41 <expand macro="list_string_san" name="out"/> 40 <expand macro="list_string_san" name="out"/>
42 </param> 41 </param>
43 <param argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1"> 42 <param argument="-mz" type="text" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
44 <expand macro="list_string_san" name="mz"/> 43 <expand macro="list_string_san" name="mz"/>
45 </param> 44 </param>
46 <param argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help=""> 45 <param argument="-rt" type="text" value=":" label="retention time range of spectra to extract" help="">
47 <expand macro="list_string_san" name="rt"/> 46 <expand macro="list_string_san" name="rt"/>
48 </param> 47 </param>
49 <param argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help=""> 48 <param argument="-level" type="text" value="1,2,3" label="MS levels to extract" help="">
50 <expand macro="list_string_san" name="level"/> 49 <expand macro="list_string_san" name="level"/>
51 </param> 50 </param>
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 </data> 64 </data>
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_DTAExtractor_1 --> 69 <tests>
70 <!-- TOPP_DTAExtractor_1 -->
71 <test expect_num_outputs="1"> 71 <test expect_num_outputs="1">
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>
82 <output name="ctd_out" ftype="xml"> 82 <output name="ctd_out" ftype="xml">
83 <assert_contents> 83 <assert_contents>
84 <is_valid_xml/> 84 <is_valid_xml/>
85 </assert_contents> 85 </assert_contents>
86 </output> 86 </output>
87 <assert_stdout>
88 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
89 </assert_stdout>
87 </test> 90 </test>
88 <!-- TOPP_DTAExtractor_2 --> 91 <!-- TOPP_DTAExtractor_2 -->
89 <test expect_num_outputs="1"> 92 <test expect_num_outputs="1">
90 <section name="adv_opts"> 93 <section name="adv_opts">
91 <param name="force" value="false"/> 94 <param name="force" value="false"/>
100 <output name="ctd_out" ftype="xml"> 103 <output name="ctd_out" ftype="xml">
101 <assert_contents> 104 <assert_contents>
102 <is_valid_xml/> 105 <is_valid_xml/>
103 </assert_contents> 106 </assert_contents>
104 </output> 107 </output>
108 <assert_stdout>
109 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
110 </assert_stdout>
105 </test> 111 </test>
106 <!-- TOPP_DTAExtractor_3 --> 112 <!-- TOPP_DTAExtractor_3 -->
107 <test expect_num_outputs="1"> 113 <test expect_num_outputs="1">
108 <section name="adv_opts"> 114 <section name="adv_opts">
109 <param name="force" value="false"/> 115 <param name="force" value="false"/>
118 <output name="ctd_out" ftype="xml"> 124 <output name="ctd_out" ftype="xml">
119 <assert_contents> 125 <assert_contents>
120 <is_valid_xml/> 126 <is_valid_xml/>
121 </assert_contents> 127 </assert_contents>
122 </output> 128 </output>
129 <assert_stdout>
130 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
131 </assert_stdout>
123 </test> 132 </test>
124 </tests> 133 </tests>
125 <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format. 134 <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format.
126 135
127 136
128 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DTAExtractor.html]]></help> 137 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DTAExtractor.html]]></help>
129 <expand macro="references"/> 138 <expand macro="references"/>
130 </tool> 139 </tool>