Mercurial > repos > galaxyp > openms_precursormasscorrector
view PrecursorMassCorrector.xml @ 13:b71e9103d269 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:28:46 +0000 |
parents | 35123b3fe2f2 |
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<!--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: [Mass Correction and Calibration]--> <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information</description> <macros> <token name="@EXECUTABLE@">PrecursorMassCorrector</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ @EXT_FOO@ #import re ## Preprocessing mkdir in && cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $feature_in: mkdir feature_in && cp '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' && #end if ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__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($feature_in.ext)' #end if ## Postprocessing && mv 'out/output.${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 argument="-in" type="data" format="mzml" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/> <param 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 argument="-precursor_mass_tolerance" type="float" 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 argument="-max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/> <param argument="-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=""/> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" 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> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <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> <tests> <!-- TOPP_PrecursorMassCorrector_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="max_charge" value="3"/> <param name="intensity_threshold" value="-1.0"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="PrecursorMassCorrector_1_input.mzML"/> <output name="out" value="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="precursor_mass_tolerance" value="1.5"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> <assert_stdout> <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> </assert_stdout> </test> </tests> <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information. For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PrecursorMassCorrector.html]]></help> <expand macro="references"/> </tool>