Mercurial > repos > galaxyp > openms_mapnormalizer

comparison MapNormalizer.xml @ 14:4b603a44b009 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 21:43:20 +0000
parents 35acd0d34d48
children
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equal deleted inserted replaced
13:35acd0d34d48 14:4b603a44b009
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: [Signal processing and preprocessing]--> 2 <!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
4 <tool id="MapNormalizer" name="MapNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MapNormalizer" name="MapNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Normalizes peak intensities in an MS run.</description> 4 <description>Normalizes peak intensities in an MS run</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MapNormalizer</token> 6 <token name="@EXECUTABLE@">MapNormalizer</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 &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
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>
54 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 53 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
55 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 54 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
56 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 55 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
57 </data> 56 </data>
58 </outputs> 57 </outputs>
59 <tests><!-- TOPP_MapNormalizer_1 --> 58 <tests>
59 <!-- TOPP_MapNormalizer_1 -->
60 <test expect_num_outputs="2"> 60 <test expect_num_outputs="2">
61 <section name="adv_opts"> 61 <section name="adv_opts">
62 <param name="force" value="false"/> 62 <param name="force" value="false"/>
63 <param name="test" value="true"/> 63 <param name="test" value="true"/>
64 </section> 64 </section>
65 <param name="in" value="MapNormalizer_input.mzML"/> 65 <param name="in" value="MapNormalizer_input.mzML"/>
66 <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 66 <output name="out" value="MapNormalizer_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
67 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 67 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
68 <output name="ctd_out" ftype="xml"> 68 <output name="ctd_out" ftype="xml">
69 <assert_contents> 69 <assert_contents>
70 <is_valid_xml/> 70 <is_valid_xml/>
71 </assert_contents> 71 </assert_contents>
72 </output> 72 </output>
73 <assert_stdout>
74 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
75 </assert_stdout>
73 </test> 76 </test>
74 </tests> 77 </tests>
75 <help><![CDATA[Normalizes peak intensities in an MS run. 78 <help><![CDATA[Normalizes peak intensities in an MS run.
76 79
77 80
78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapNormalizer.html]]></help> 81 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapNormalizer.html]]></help>
79 <expand macro="references"/> 82 <expand macro="references"/>
80 </tool> 83 </tool>