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view OpenSwathDIAPreScoring.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author | bgruening |
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date | Wed, 27 Jan 2016 10:06:49 -0500 |
parents | 3d84209d3178 |
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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: [Targeted Experiments]--> <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.0.0"> <description>Scoring spectra using the DIA scores.</description> <macros> <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>OpenSwathDIAPreScoring #if $param_tr: -tr $param_tr #end if #if $param_out: -out $param_out #end if -swath_files #for token in $param_swath_files: $token #end for #if $param_min_upper_edge_dist: -min_upper_edge_dist $param_min_upper_edge_dist #end if -threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param format="traml" help="(-tr) " label="transition file" name="param_tr" optional="False" type="data"/> <param format="mzml" help="(-swath_files) If present, SWATH specific scoring will be applied" label="Swath files that were used to extract the transitions" multiple="true" name="param_swath_files" optional="True" size="30" type="data"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-min_upper_edge_dist) " label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" name="param_min_upper_edge_dist" type="float" value="0.0"/> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> </expand> </inputs> <outputs> <data format="tabular" name="param_out"/> </outputs> <help>Scoring spectra using the DIA scores. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html</help> </tool>