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view MapAlignerIdentification.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: [Map Alignment]--> <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="2.0.0"> <description>Corrects retention time distortions between maps based on common peptide identifications.</description> <macros> <token name="@EXECUTABLE@">MapAlignerIdentification</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>MapAlignerIdentification -in #for token in $param_in: $token #end for #if $rep_param_out: -out #for token in $rep_param_out: #if " " in str(token): "$token.param_out" #else $token.param_out #end if #end for #end if #if $rep_param_trafo_out: -trafo_out #for token in $rep_param_trafo_out: #if " " in str(token): "$token.param_trafo_out" #else $token.param_trafo_out #end if #end for #end if -threads \${GALAXY_SLOTS:-24} #if $param_reference_file: -reference:file $param_reference_file #end if #if $param_reference_index: -reference:index $param_reference_index #end if #if $param_algorithm_peptide_score_threshold: -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold #end if #if $param_algorithm_min_run_occur: -algorithm:min_run_occur $param_algorithm_min_run_occur #end if #if $param_algorithm_max_rt_shift: -algorithm:max_rt_shift $param_algorithm_max_rt_shift #end if #if $param_algorithm_use_unassigned_peptides: -algorithm:use_unassigned_peptides #end if #if $param_algorithm_use_feature_rt: -algorithm:use_feature_rt #end if #if $param_model_type: -model:type #if " " in str($param_model_type): "$param_model_type" #else $param_model_type #end if #end if #if $param_model_linear_symmetric_regression: -model:linear:symmetric_regression #end if #if $param_model_b_spline_wavelength: -model:b_spline:wavelength $param_model_b_spline_wavelength #end if #if $param_model_b_spline_num_nodes: -model:b_spline:num_nodes $param_model_b_spline_num_nodes #end if #if $param_model_b_spline_extrapolate: -model:b_spline:extrapolate #if " " in str($param_model_b_spline_extrapolate): "$param_model_b_spline_extrapolate" #else $param_model_b_spline_extrapolate #end if #end if #if $param_model_b_spline_boundary_condition: -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition #end if #if $param_model_interpolated_interpolation_type: -model:interpolated:interpolation_type #if " " in str($param_model_interpolated_interpolation_type): "$param_model_interpolated_interpolation_type" #else $param_model_interpolated_interpolation_type #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param format="xml,consensusxml" help="(-in) " label="Input files to align (all must have the same file type)" multiple="true" name="param_in" optional="False" size="30" type="data"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param format="xml,consensusxml" help="(-file) " label="File to use as reference" name="param_reference_file" optional="True" type="data"/> <param help="(-index) <br>If '0', no explicit reference is set - the algorithm will select a reference" label="Use one of the input files as reference ('1' for the first file, etc.)" min="0" name="param_reference_index" optional="True" type="integer" value="0"/> <param help="(-peptide_score_threshold) <br>Select a value that allows only 'high confidence' matches" label="Score threshold for peptide hits to be used in the alignment" name="param_algorithm_peptide_score_threshold" type="float" value="0.0"/> <param help="(-min_run_occur) reference, if any) a peptide must occur in to be used for the alignment. <br>Unless you have very few runs or identifications, increase this value to focus on more informative peptides" label="Minimum number of runs (incl" min="2" name="param_algorithm_min_run_occur" optional="True" type="integer" value="2"/> <param help="(-max_rt_shift) reference). Peptides with higher shifts (outliers) are not used to compute the alignment. <br>If 0, no limit (disable filter); if > 1, the final value in seconds; if <= 1, taken as a fraction of the range of the reference RT scale" label="Maximum realistic RT difference for a peptide (median per run vs" min="0.0" name="param_algorithm_max_rt_shift" optional="True" type="float" value="0.5"/> <param checked="true" falsevalue="" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used" label="Should unassigned peptide identifications be used when computing an alignment of feature maps?" name="param_algorithm_use_unassigned_peptides" optional="True" truevalue="-algorithm:use_unassigned_peptides" type="boolean"/> <param checked="false" falsevalue="" help="(-use_feature_rt) If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used. <br>Precludes 'use_unassigned_peptides'" label="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" name="param_algorithm_use_feature_rt" optional="True" truevalue="-algorithm:use_feature_rt" type="boolean"/> <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="b_spline"> <option value="linear">linear</option> <option value="b_spline">b_spline</option> <option value="interpolated">interpolated</option> </param> <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Perform linear regression on 'y - x' vs" name="param_model_linear_symmetric_regression" optional="True" truevalue="-model:linear:symmetric_regression" type="boolean"/> <param help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" min="0.0" name="param_model_b_spline_wavelength" optional="True" type="float" value="0.0"/> <param help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing" label="Number of nodes for B-spline fitting" min="0" name="param_model_b_spline_num_nodes" optional="True" type="integer" value="5"/> <param help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)" label="Method to use for extrapolation beyond the original data range" name="param_model_b_spline_extrapolate" optional="True" type="select" value="linear"> <option value="linear">linear</option> <option value="b_spline">b_spline</option> <option value="constant">constant</option> <option value="global_linear">global_linear</option> </param> <param help="(-boundary_condition) " label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" max="2" min="0" name="param_model_b_spline_boundary_condition" optional="True" type="integer" value="2"/> <param help="(-interpolation_type) " label="Type of interpolation to apply" name="param_model_interpolated_interpolation_type" optional="True" type="select" value="cspline"> <option value="linear">linear</option> <option value="cspline">cspline</option> <option value="akima">akima</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"/> </expand> </inputs> <outputs> <data format="input" metadata_source="param_in" name="param_out"/> <data format="trafoxml" name="param_trafo_out"/> </outputs> <help>Corrects retention time distortions between maps based on common peptide identifications. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help> </tool>