Mercurial > repos > galaxyp > openms_mapnormalizer

comparison MapNormalizer.xml @ 13:35acd0d34d48 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:23:57 +0000
parents 7d45a120519f
children 4b603a44b009
comparison
equal deleted inserted replaced
12:d913c83081e1 13:35acd0d34d48
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 2 <!--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]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="MapNormalizer" name="MapNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MapNormalizer" name="MapNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Normalizes peak intensities in an MS run.</description> 5 <description>Normalizes peak intensities in an MS run.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapNormalizer</token> 7 <token name="@EXECUTABLE@">MapNormalizer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
45 <expand macro="adv_opts_macro"> 43 <expand macro="adv_opts_macro">
46 <param name="force" 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=""/>
47 <param name="test" 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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
48 <expand macro="list_string_san"/> 46 <expand macro="list_string_san" name="test"/>
49 </param> 47 </param>
50 </expand> 48 </expand>
51 <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">
52 <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>
53 </param> 51 </param>
56 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 54 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 55 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 56 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
59 </data> 57 </data>
60 </outputs> 58 </outputs>
61 <tests> 59 <tests><!-- TOPP_MapNormalizer_1 -->
62 <expand macro="autotest_MapNormalizer"/> 60 <test expect_num_outputs="2">
63 <expand macro="manutest_MapNormalizer"/> 61 <section name="adv_opts">
62 <param name="force" value="false"/>
63 <param name="test" value="true"/>
64 </section>
65 <param name="in" value="MapNormalizer_input.mzML"/>
66 <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
67 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
68 <output name="ctd_out" ftype="xml">
69 <assert_contents>
70 <is_valid_xml/>
71 </assert_contents>
72 </output>
73 </test>
64 </tests> 74 </tests>
65 <help><![CDATA[Normalizes peak intensities in an MS run. 75 <help><![CDATA[Normalizes peak intensities in an MS run.
66 76
67 77
68 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapNormalizer.html]]></help> 78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapNormalizer.html]]></help>
69 <expand macro="references"/> 79 <expand macro="references"/>
70 </tool> 80 </tool>