Mercurial > repos > galaxyp > openms_additiveseries
view AdditiveSeries.xml @ 5:1604983bcadb draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 23 Aug 2017 13:38:04 -0400 |
parents | d86b95a89b12 |
children | eabed74a76bd |
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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: [Quantitation]--> <tool id="AdditiveSeries" name="AdditiveSeries" version="2.2.0"> <description>Computes an additive series to quantify a peptide in a set of samples.</description> <macros> <token name="@EXECUTABLE@">AdditiveSeries</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>AdditiveSeries -in #for token in $param_in: $token #end for #if $param_out: -out $param_out #end if #if $param_mz_tolerance: -mz_tolerance $param_mz_tolerance #end if #if $param_rt_tolerance: -rt_tolerance $param_rt_tolerance #end if #if $rep_param_concentrations: -concentrations #for token in $rep_param_concentrations: #if " " in str(token): "$token.param_concentrations" #else $token.param_concentrations #end if #end for #end if #if $param_feature_rt: -feature_rt $param_feature_rt #end if #if $param_feature_mz: -feature_mz $param_feature_mz #end if #if $param_standard_rt: -standard_rt $param_standard_rt #end if #if $param_standard_mz: -standard_mz $param_standard_mz #end if #if $param_plot_write_gnuplot_output: -plot:write_gnuplot_output #end if #if $param_plot_out_gp: -plot:out_gp "$param_plot_out_gp" #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param name="param_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_mz_tolerance" type="float" value="1.0" label="Tolerance in m/z dimension" help="(-mz_tolerance) "/> <param name="param_rt_tolerance" type="float" value="1.0" label="Tolerance in RT dimension" help="(-rt_tolerance) "/> <repeat name="rep_param_concentrations" min="1" max="1" title="param_concentrations"> <param name="param_concentrations" type="text" size="30" value="0" label="List of spiked concentrations" help="(-concentrations) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param name="param_feature_rt" type="float" value="-1.0" label="RT position of the feature" help="(-feature_rt) "/> <param name="param_feature_mz" type="float" value="-1.0" label="m/z position of the feature" help="(-feature_mz) "/> <param name="param_standard_rt" type="float" value="-1.0" label="RT position of the standard" help="(-standard_rt) "/> <param name="param_standard_mz" type="float" value="-1.0" label="m/z position of the standard" help="(-standard_mz) "/> <param name="param_plot_write_gnuplot_output" display="radio" type="boolean" truevalue="-plot:write_gnuplot_output" falsevalue="" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output) "/> <param name="param_plot_out_gp" type="text" size="30" label="base file name (3 files with different extensions are created)" help="(-out_gp) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <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) "/> </expand> </inputs> <outputs> <data name="param_out" format="xml"/> </outputs> <help>Computes an additive series to quantify a peptide in a set of samples. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html</help> </tool>