Mercurial > repos > galaxyp > openms_speclibcreator
diff SpecLibCreator.xml @ 9:70105532a580 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 20:00:46 +0000 |
parents | 1ea89972c6c7 |
children | 5d837ca93d0e |
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--- a/SpecLibCreator.xml Fri May 17 10:14:02 2019 -0400 +++ b/SpecLibCreator.xml Wed Sep 09 20:00:46 2020 +0000 @@ -1,59 +1,79 @@ <?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]--> -<tool id="SpecLibCreator" name="SpecLibCreator" version="2.3.0"> +<tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Creates an MSP formatted spectral library.</description> <macros> <token name="@EXECUTABLE@">SpecLibCreator</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[SpecLibCreator + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir info && +ln -s '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' && +mkdir spec && +ln -s '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' && +mkdir out && + +## Main program call -#if $param_info: - -info $param_info -#end if -#if $param_itemseperator: - -itemseperator "$param_itemseperator" -#end if -#if $param_itemenclosed: - -itemenclosed -#end if -#if $param_spec: - -spec $param_spec -#end if -#if $param_out: - -out $param_out -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-info +'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' +-spec +'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' +-out +'out/output.${gxy2omsext("msp")}' + +## Postprocessing +&& mv 'out/output.${gxy2omsext("msp")}' '$out' +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc" help="(-info) "/> - <param name="param_itemseperator" type="text" size="30" value="," label=" Separator between items. e.g. ," help="(-itemseperator) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="info" argument="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/> + <param name="itemseperator" argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help=""> + <expand macro="list_string_san"/> </param> - <param name="param_itemenclosed" display="radio" type="boolean" truevalue="-itemenclosed" falsevalue="" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed" help="(-itemenclosed) e.g. '$peptide$,$run$"/> - <param name="param_spec" type="data" format="mzData,mzxml" optional="False" label="spectra" help="(-spec) "/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="itemenclosed" argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/> + <param name="spec" argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="msp"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="msp"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Creates an MSP formatted spectral library. + <tests> + <expand macro="autotest_SpecLibCreator"/> + <expand macro="manutest_SpecLibCreator"/> + </tests> + <help><![CDATA[Creates an MSP formatted spectral library. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SpecLibCreator.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_SpecLibCreator.html]]></help> + <expand macro="references"/> </tool>