Mercurial > repos > bgruening > openms
view FeatureLinkerUnlabeledQT.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author | bgruening |
---|---|
date | Wed, 27 Jan 2016 10:06:49 -0500 |
parents | 3d84209d3178 |
children |
line wrap: on
line source
<?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: [Map Alignment]--> <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="2.0.0"> <description>Groups corresponding features from multiple maps.</description> <macros> <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>FeatureLinkerUnlabeledQT -in #for token in $param_in: $token #end for #if $param_out: -out $param_out #end if #if $param_keep_subelements: -keep_subelements #end if -threads \${GALAXY_SLOTS:-24} #if $param_algorithm_use_identifications: -algorithm:use_identifications #end if #if $param_algorithm_ignore_charge: -algorithm:ignore_charge #end if #if $param_algorithm_distance_RT_max_difference: -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference #end if #if $param_algorithm_distance_MZ_max_difference: -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference #end if #if $param_algorithm_distance_MZ_unit: -algorithm:distance_MZ:unit #if " " in str($param_algorithm_distance_MZ_unit): "$param_algorithm_distance_MZ_unit" #else $param_algorithm_distance_MZ_unit #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #if $adv_opts.param_algorithm_distance_RT_exponent: -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent #end if #if $adv_opts.param_algorithm_distance_RT_weight: -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight #end if #if $adv_opts.param_algorithm_distance_MZ_exponent: -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent #end if #if $adv_opts.param_algorithm_distance_MZ_weight: -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight #end if #if $adv_opts.param_algorithm_distance_intensity_exponent: -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent #end if #if $adv_opts.param_algorithm_distance_intensity_weight: -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight #end if #end if </command> <inputs> <param format="xml,consensusxml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param checked="false" falsevalue="" help="(-keep_subelements) " label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" name="param_keep_subelements" optional="True" truevalue="-keep_subelements" type="boolean"/> <param checked="false" falsevalue="" help="(-use_identifications) " label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" name="param_algorithm_use_identifications" optional="True" truevalue="-algorithm:use_identifications" type="boolean"/> <param checked="false" falsevalue="" help="(-ignore_charge) " label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" name="param_algorithm_ignore_charge" optional="True" truevalue="-algorithm:ignore_charge" type="boolean"/> <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_distance_RT_max_difference" optional="True" type="float" value="100.0"/> <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_distance_MZ_max_difference" optional="True" type="float" value="0.3"/> <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_distance_MZ_unit" optional="True" type="select" value="Da"> <option value="Da">Da</option> <option value="ppm">ppm</option> </param> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> <param help="(-exponent) " label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_RT_exponent" optional="True" type="float" value="1.0"/> <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_distance_RT_weight" optional="True" type="float" value="1.0"/> <param help="(-exponent) " label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_MZ_exponent" optional="True" type="float" value="2.0"/> <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_distance_MZ_weight" optional="True" type="float" value="1.0"/> <param help="(-exponent) " label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_intensity_exponent" optional="True" type="float" value="1.0"/> <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_distance_intensity_weight" optional="True" type="float" value="0.0"/> </expand> </inputs> <outputs> <data format="consensusxml" name="param_out"/> </outputs> <help>Groups corresponding features from multiple maps. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeledQT.html</help> </tool>