Mercurial > repos > galaxyp > openms_demeanderize

comparison DeMeanderize.xml @ 17:2425a98560f5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:01:59 +0000
parents c64f929ec2bf
children 17547aceaf40
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16:d2852a9e5550 17:2425a98560f5
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="DeMeanderize" name="DeMeanderize" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="DeMeanderize" name="DeMeanderize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Orders the spectra of MALDI spotting plates correctly.</description> 5 <description>Orders the spectra of MALDI spotting plates correctly.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">DeMeanderize</token> 7 <token name="@EXECUTABLE@">DeMeanderize</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 experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="Input experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/>
45 <param name="num_spots_per_row" argument="-num_spots_per_row" type="integer" optional="true" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/> 43 <param argument="-num_spots_per_row" type="integer" optional="true" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/>
46 <expand macro="adv_opts_macro"> 44 <expand macro="adv_opts_macro">
47 <param name="RT_distance" argument="-RT_distance" type="float" optional="true" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/> 45 <param argument="-RT_distance" type="float" optional="true" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/>
48 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 46 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
49 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 47 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
50 <expand macro="list_string_san"/> 48 <expand macro="list_string_san" name="test"/>
51 </param> 49 </param>
52 </expand> 50 </expand>
53 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 51 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
54 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 52 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
55 </param> 53 </param>
58 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 56 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
59 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
60 <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>
61 </data> 59 </data>
62 </outputs> 60 </outputs>
63 <tests> 61 <tests><test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->
64 <expand macro="autotest_DeMeanderize"/> 62 <param name="adv_opts|test" value="true"/>
65 <expand macro="manutest_DeMeanderize"/> 63 <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
66 </tests> 64 <output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
65 </test>
66 </tests>
67 <help><![CDATA[Orders the spectra of MALDI spotting plates correctly. 67 <help><![CDATA[Orders the spectra of MALDI spotting plates correctly.
68 68
69 69
70 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DeMeanderize.html]]></help> 70 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DeMeanderize.html]]></help>
71 <expand macro="references"/> 71 <expand macro="references"/>
72 </tool> 72 </tool>