Mercurial > repos > galaxyp > openms_assaygeneratormetabo

comparison AssayGeneratorMetabo.xml @ 4:11ac8ae77fb7 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 16:56:34 +0000
parents d30e724536fc
children 83f5e5c1209c
comparison
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3:200e9206e53a 4:11ac8ae77fb7
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="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy1" profile="20.05">
5 <description>Assay library generation from DDA data (Metabolomics)</description> 5 <description>Assay library generation from DDA data (Metabolomics)</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">AssayGeneratorMetabo</token> 7 <token name="@EXECUTABLE@">AssayGeneratorMetabo</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import> 9 <import>macros_autotest.xml</import>
40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
41 && mv '@EXECUTABLE@.ctd' '$ctd_out' 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command> 42 #end if]]></command>
43 <configfiles> 43 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile> 45 <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>
46 </configfiles> 46 </configfiles>
47 <inputs> 47 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/> 48 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
49 <param name="in_id" argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/> 49 <param name="in_id" argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
50 <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)"> 50 <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)">
69 <param name="use_known_unknowns" argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/> 69 <param name="use_known_unknowns" argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/>
70 <param name="min_transitions" argument="-min_transitions" type="integer" optional="true" value="3" label="Minimal number of transitions" help=""/> 70 <param name="min_transitions" argument="-min_transitions" type="integer" optional="true" value="3" label="Minimal number of transitions" help=""/>
71 <param name="max_transitions" argument="-max_transitions" type="integer" optional="true" value="3" label="Maximal number of transitions" help=""/> 71 <param name="max_transitions" argument="-max_transitions" type="integer" optional="true" value="3" label="Maximal number of transitions" help=""/>
72 <param name="cosine_similarity_threshold" argument="-cosine_similarity_threshold" type="float" optional="true" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/> 72 <param name="cosine_similarity_threshold" argument="-cosine_similarity_threshold" type="float" optional="true" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/>
73 <param name="transition_threshold" argument="-transition_threshold" type="float" optional="true" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/> 73 <param name="transition_threshold" argument="-transition_threshold" type="float" optional="true" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/>
74 <param name="out_workspace_directory" argument="-out_workspace_directory" type="text" optional="true" value="" label="Output directory for SIRIUS workspace" help="">
75 <expand macro="list_string_san"/>
76 </param>
77 <section name="deisotoping" title="deisotoping" help="" expanded="false"> 74 <section name="deisotoping" title="deisotoping" help="" expanded="false">
78 <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/> 75 <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/>
79 <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" optional="true" value="1.0" label="Tolerance used to match isotopic peaks" help=""/> 76 <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" optional="true" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
80 <param name="fragment_unit" argument="-deisotoping:fragment_unit" display="radio" type="select" optional="false" label="Unit of the fragment tolerance" help=""> 77 <param name="fragment_unit" argument="-deisotoping:fragment_unit" display="radio" type="select" optional="false" label="Unit of the fragment tolerance" help="">
81 <option value="ppm" selected="true">ppm</option> 78 <option value="ppm" selected="true">ppm</option>