Mercurial > repos > galaxyp > openms_clustermasstraces

comparison ClusterMassTraces.xml @ 5:3350a9c0631a 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 21:44:13 +0000
parents 10c41ad01df5
children
comparison
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4:10c41ad01df5 5:3350a9c0631a
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: [Utilities]--> 2 <!--Proposed Tool Section: [Misc / Helpers]-->
4 <tool id="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Creates pseudo spectra.</description> 4 <description>Creates pseudo spectra</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">ClusterMassTraces</token> 6 <token name="@EXECUTABLE@">ClusterMassTraces</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="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/> 41 <param argument="-in" type="data" format="consensusxml" label="Mass traces" help=" select consensusxml data sets(s)"/>
43 <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/> 42 <param argument="-min_pearson_correlation" type="float" value="0.7" label="Minimal pearson correlation score" help=""/>
44 <param argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/> 43 <param argument="-min_peak_nr" type="integer" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
45 <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/> 44 <param argument="-max_lag" type="integer" value="1" label="Maximal lag" 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=""/> 45 <param argument="-max_rt_apex_difference" type="float" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
47 <param argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/> 46 <param argument="-max_intensity_cutoff" type="float" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
48 <param argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/> 47 <param argument="-add_precursor" type="float" value="0.0" label="Add a precursor mass" help=""/>
49 <expand macro="adv_opts_macro"> 48 <expand macro="adv_opts_macro">
50 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
51 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 50 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
52 <expand macro="list_string_san" name="test"/> 51 <expand macro="list_string_san" name="test"/>
53 </param> 52 </param>
54 </expand> 53 </expand>
55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
60 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 59 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
62 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
63 </data> 62 </data>
64 </outputs> 63 </outputs>
65 <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> 64 <tests>
66 <param name="adv_opts|test" value="true"/> 65 <test expect_num_outputs="1">
67 <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> 66 <!-- test with arbitarily chosen consensusXML -->
68 <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/> 67 <param name="adv_opts|test" value="true"/>
69 </test> 68 <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
70 </tests> 69 <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
70 </test>
71 </tests>
71 <help><![CDATA[Creates pseudo spectra. 72 <help><![CDATA[Creates pseudo spectra.
72 73
73 74
74 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTraces.html]]></help> 75 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ClusterMassTraces.html]]></help>
75 <expand macro="references"/> 76 <expand macro="references"/>
76 </tool> 77 </tool>