Mercurial > repos > galaxyp > openms_highresprecursormasscorrector
view HighResPrecursorMassCorrector.xml @ 8:95b53cafbd29 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author | galaxyp |
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date | Tue, 20 Mar 2018 14:48:46 -0400 |
parents | 26304be6f0a6 |
children | a777f667393e |
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<?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="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="2.3.0"> <description>Corrects the precursor mass and charge determined by the instrument software.</description> <macros> <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>HighResPrecursorMassCorrector #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_out_csv: -out_csv $param_out_csv #end if #if $param_feature_in: -feature:in $param_feature_in #end if #if $param_feature_mz_tolerance: -feature:mz_tolerance $param_feature_mz_tolerance #end if #if $param_feature_mz_tolerance_unit: -feature:mz_tolerance_unit #if " " in str($param_feature_mz_tolerance_unit): "$param_feature_mz_tolerance_unit" #else $param_feature_mz_tolerance_unit #end if #end if #if $param_feature_rt_tolerance: -feature:rt_tolerance $param_feature_rt_tolerance #end if #if $param_feature_believe_charge: -feature:believe_charge #end if #if $param_feature_keep_original: -feature:keep_original #end if #if $param_feature_assign_all_matching: -feature:assign_all_matching #end if #if $param_nearest_peak_mz_tolerance: -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance #end if #if $param_nearest_peak_mz_tolerance_unit: -nearest_peak:mz_tolerance_unit #if " " in str($param_nearest_peak_mz_tolerance_unit): "$param_nearest_peak_mz_tolerance_unit" #else $param_nearest_peak_mz_tolerance_unit #end if #end if #if $param_highest_intensity_peak_mz_tolerance: -highest_intensity_peak:mz_tolerance $param_highest_intensity_peak_mz_tolerance #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #if $adv_opts.param_feature_max_trace: -feature:max_trace $adv_opts.param_feature_max_trace #end if #end if </command> <inputs> <param name="param_in" type="data" format="mzml" optional="False" label="Input file (centroided data)" help="(-in) "/> <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Features used to correct precursor masses" help="(-in) "/> <param name="param_feature_mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="(-mz_tolerance) Used to determine matching to feature mass traces"/> <param name="param_feature_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) "> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> </param> <param name="param_feature_rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help="(-rt_tolerance) "/> <param name="param_feature_believe_charge" display="radio" type="boolean" truevalue="-feature:believe_charge" falsevalue="" checked="false" optional="True" label="Assume precursor charge to be correct" help="(-believe_charge) "/> <param name="param_feature_keep_original" display="radio" type="boolean" truevalue="-feature:keep_original" falsevalue="" checked="false" optional="True" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help="(-keep_original) "/> <param name="param_feature_assign_all_matching" display="radio" type="boolean" truevalue="-feature:assign_all_matching" falsevalue="" checked="false" optional="True" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="(-assign_all_matching) Only evaluated if copies are created (feature:keep_original)"/> <param name="param_nearest_peak_mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(-mz_tolerance) (Disable method by setting value to 0.0)"/> <param name="param_nearest_peak_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) "> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> </param> <param name="param_highest_intensity_peak_mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak (Da)" help="(-mz_tolerance) Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/> <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="param_feature_max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help="(-max_trace) "/> </expand> </inputs> <outputs> <data name="param_out" format="mzml"/> <data name="param_out_csv" format="tabular"/> </outputs> <help>Corrects the precursor mass and charge determined by the instrument software. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html</help> </tool>