Mercurial > repos > galaxyp > openms_clustermasstraces

comparison ClusterMassTraces.xml @ 4:10c41ad01df5 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 19:11:57 +0000
parents 6d513a5aaa36
children 3350a9c0631a
comparison
equal deleted inserted replaced
3:c29d85d3e732 4:10c41ad01df5
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="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Creates pseudo spectra.</description> 5 <description>Creates pseudo spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ClusterMassTraces</token> 7 <token name="@EXECUTABLE@">ClusterMassTraces</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="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/> 42 <param argument="-in" type="data" format="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/>
45 <param name="min_pearson_correlation" argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/> 43 <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/>
46 <param name="min_peak_nr" argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/> 44 <param argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
47 <param name="max_lag" argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/> 45 <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/>
48 <param name="max_rt_apex_difference" argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/> 46 <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
49 <param name="max_intensity_cutoff" argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/> 47 <param argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
50 <param name="add_precursor" argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/> 48 <param argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/>
51 <expand macro="adv_opts_macro"> 49 <expand macro="adv_opts_macro">
52 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 50 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
53 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 51 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
54 <expand macro="list_string_san"/> 52 <expand macro="list_string_san" name="test"/>
55 </param> 53 </param>
56 </expand> 54 </expand>
57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
59 </param> 57 </param>
62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 60 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 62 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
65 </data> 63 </data>
66 </outputs> 64 </outputs>
67 <tests> 65 <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
68 <expand macro="autotest_ClusterMassTraces"/> 66 <param name="adv_opts|test" value="true"/>
69 <expand macro="manutest_ClusterMassTraces"/> 67 <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
70 </tests> 68 <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
69 </test>
70 </tests>
71 <help><![CDATA[Creates pseudo spectra. 71 <help><![CDATA[Creates pseudo spectra.
72 72
73 73
74 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_ClusterMassTraces.html]]></help> 74 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTraces.html]]></help>
75 <expand macro="references"/> 75 <expand macro="references"/>
76 </tool> 76 </tool>