Mercurial > repos > galaxyp > openms_qcextractor
diff QCExtractor.xml @ 13:9a527fdadffc draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
---|---|
date | Fri, 14 Jun 2024 21:29:38 +0000 |
parents | c8d22d876c75 |
children |
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--- a/QCExtractor.xml Thu Dec 01 19:00:36 2022 +0000 +++ b/QCExtractor.xml Fri Jun 14 21:29:38 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [Utilities]--> +<!--Proposed Tool Section: []--> <tool id="QCExtractor" name="QCExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Extracts a table attachment to a given qc parameter.</description> + <description>Extracts a table attachment to a given qc parameter</description> <macros> <token name="@EXECUTABLE@">QCExtractor</token> <import>macros.xml</import> @@ -15,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $run: mkdir run && - ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && + cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && #end if mkdir out_csv && @@ -47,8 +46,8 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/> - <param argument="-qp" type="text" optional="false" value="" label="Target attachment qp" help=""> + <param argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/> + <param argument="-qp" type="text" value="" label="Target attachment qp" help=""> <expand macro="list_string_san" name="qp"/> </param> <param argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/> @@ -57,7 +56,7 @@ </param> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -71,11 +70,12 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!--TODO--> -</tests> + <tests> + <!--TODO--> + </tests> <help><![CDATA[Extracts a table attachment to a given qc parameter. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCExtractor.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCExtractor.html]]></help> <expand macro="references"/> </tool>