Mercurial > repos > galaxyp > openms_precursormasscorrector
diff PrecursorMassCorrector.xml @ 0:7788e4d10cc6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:52:00 -0500 |
parents | |
children | 5037d5ad9aad |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PrecursorMassCorrector.xml Wed Mar 01 12:52:00 2017 -0500 @@ -0,0 +1,56 @@ +<?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="2.1.0"> + <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>