Mercurial > repos > galaxyp > openms_precursormasscorrector
diff PrecursorMassCorrector.xml @ 8:315dca04e06f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 20:04:40 +0000 |
parents | 79760732d9e3 |
children | e15d84652dba |
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--- a/PrecursorMassCorrector.xml Fri May 17 10:25:32 2019 -0400 +++ b/PrecursorMassCorrector.xml Wed Sep 09 20:04:40 2020 +0000 @@ -1,56 +1,82 @@ <?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: [Signal processing and preprocessing]--> -<tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.3.0"> +<tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description> <macros> <token name="@EXECUTABLE@">PrecursorMassCorrector</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[PrecursorMassCorrector + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_feature_in: - -feature_in $param_feature_in -#end if -#if $param_precursor_mass_tolerance: - -precursor_mass_tolerance $param_precursor_mass_tolerance +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && +#if $feature_in: + mkdir feature_in && + ln -s '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' && #end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_max_charge: - -max_charge $adv_opts.param_max_charge -#end if - #if $adv_opts.param_intensity_threshold: - -intensity_threshold $adv_opts.param_intensity_threshold -#end if - #if $adv_opts.param_force: - -force -#end if + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-out +'out/output.${gxy2omsext("mzml")}' +#if $feature_in: + -feature_in + 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' #end if -]]></command> + +## Postprocessing +&& mv 'out/output.${gxy2omsext("mzml")}' '$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_in" type="data" format="mzml" optional="False" label="Input mzML file containing the spectra" help="(-in) "/> - <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries <br>will be matched to the feature m/z values if possible" help="(-feature_in) "/> - <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected; <br>this value should be set to the instruments selection window" help="(-precursor_mass_tolerance) "/> - <expand macro="advanced_options"> - <param name="param_max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help="(-max_charge) "/> - <param name="param_intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help="(-intensity_threshold) "/> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/> + <param name="feature_in" argument="-feature_in" type="data" format="featurexml" optional="true" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries" help="will be matched to the feature m/z values if possible select featurexml data sets(s)"/> + <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/> + <expand macro="adv_opts_macro"> + <param name="max_charge" argument="-max_charge" type="integer" optional="true" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/> + <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/> + <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="mzml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Corrects the precursor entries of MS/MS spectra, by using MS1 information. + <tests> + <expand macro="autotest_PrecursorMassCorrector"/> + <expand macro="manutest_PrecursorMassCorrector"/> + </tests> + <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PrecursorMassCorrector.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_PrecursorMassCorrector.html]]></help> + <expand macro="references"/> </tool>