Mercurial > repos > galaxyp > openms_idmassaccuracy
view IDMassAccuracy.xml @ 7:2c96363c5a17 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author | galaxyp |
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date | Mon, 12 Feb 2018 13:03:04 -0500 |
parents | 49dcff453eee |
children | 86f5365280dd |
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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: [Utilities]--> <tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.3.0"> <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description> <macros> <token name="@EXECUTABLE@">IDMassAccuracy</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>IDMassAccuracy -in #for token in $param_in: $token #end for -id_in #for token in $param_id_in: $token #end for #if $param_precursor_out: -precursor_out $param_precursor_out #end if #if $rep_param_precursor_columns: -precursor_columns #for token in $rep_param_precursor_columns: #if " " in str(token): "$token.param_precursor_columns" #else $token.param_precursor_columns #end if #end for #end if #if $param_precursor_error_ppm: -precursor_error_ppm #end if #if $param_fragment_out: -fragment_out $param_fragment_out #end if #if $rep_param_fragment_columns: -fragment_columns #for token in $rep_param_fragment_columns: #if " " in str(token): "$token.param_fragment_columns" #else $token.param_fragment_columns #end if #end for #end if #if $param_fragment_error_ppm: -fragment_error_ppm #end if #if $param_fragment_mass_tolerance: -fragment_mass_tolerance $param_fragment_mass_tolerance #end if #if $param_separator: -separator "$param_separator" #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_number_of_bins: -number_of_bins $adv_opts.param_number_of_bins #end if #if $adv_opts.param_generate_gnuplot_scripts: -generate_gnuplot_scripts #end if #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns"> <param name="param_precursor_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) "> <option value="MassDifference">MassDifference</option> </param> </repeat> <param name="param_precursor_error_ppm" display="radio" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/> <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns"> <param name="param_fragment_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) "> <option value="MassDifference">MassDifference</option> </param> </repeat> <param name="param_fragment_error_ppm" display="radio" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/> <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/> <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <expand macro="advanced_options"> <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/> <param name="param_generate_gnuplot_scripts" display="radio" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/> <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_precursor_out" format="tabular"/> <data name="param_fragment_out" format="tabular"/> </outputs> <help>Calculates a distribution of the mass error from given mass spectra and IDs. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html</help> </tool>