Mercurial > repos > galaxyp > openms_siriusadapter

comparison SiriusAdapter.xml @ 8:2d655933d65f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 14 Dec 2020 16:53:26 +0000
parents ac6f09817679
children 0c27444604dd
comparison
equal deleted inserted replaced
7:d784e23cc91c 8:2d655933d65f
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="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description> 5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SiriusAdapter</token> 7 <token name="@EXECUTABLE@">SiriusAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import> 9 <import>macros_autotest.xml</import>
73 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 73 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
74 && mv '@EXECUTABLE@.ctd' '$ctd_out' 74 && mv '@EXECUTABLE@.ctd' '$ctd_out'
75 #end if]]></command> 75 #end if]]></command>
76 <configfiles> 76 <configfiles>
77 <inputs name="args_json" data_style="paths"/> 77 <inputs name="args_json" data_style="paths"/>
78 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile> 78 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile>
79 </configfiles> 79 </configfiles>
80 <inputs> 80 <inputs>
81 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/> 81 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
82 <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/> 82 <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
83 <param name="out_workspace_directory" argument="-out_workspace_directory" type="text" optional="true" value="" label="Output directory for SIRIUS workspace" help="">
84 <expand macro="list_string_san"/>
85 </param>
86 <section name="preprocessing" title="Preprocessing" help="" expanded="false"> 83 <section name="preprocessing" title="Preprocessing" help="" expanded="false">
87 <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Features have to have at least x MassTraces" help="To use this parameter feature_only is neccessary"/> 84 <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Features have to have at least x MassTraces" help="To use this parameter feature_only is neccessary"/>
88 <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="0.005" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/> 85 <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="0.005" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
89 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help=""> 86 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help="">
90 <option value="Da" selected="true">Da</option> 87 <option value="Da" selected="true">Da</option>