Mercurial > repos > galaxyp > openms_precursormasscorrector
view PrecursorMassCorrector.xml @ 2:fe8e0898006b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author | galaxyp |
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date | Wed, 18 Oct 2017 15:39:32 -0400 |
parents | 5037d5ad9aad |
children | 8a8511f63d74 |
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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 CTD2Galaxy.--> <!--Proposed Tool Section: [Signal processing and preprocessing]--> <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.2.0"> <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="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>PrecursorMassCorrector #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 #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 #end if </command> <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) "/> </expand> </inputs> <outputs> <data name="param_out" format="mzml"/> </outputs> <help>Corrects the precursor entries of MS/MS spectra, by using MS1 information. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html</help> </tool>