Mercurial > repos > galaxyp > openms
diff MapAlignerIdentification.xml @ 0:3070d71e0e5c draft
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| author | bgruening |
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| date | Thu, 16 Apr 2015 08:37:04 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MapAlignerIdentification.xml Thu Apr 16 08:37:04 2015 -0400 @@ -0,0 +1,153 @@ +<?xml version='1.0' encoding='UTF-8'?> +<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="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 name="param_in" type="data" format="featurexml,consensusxml,idxml" multiple="true" optional="False" size="30" label="Input files separated by blanks (all must have the same file type)" help="(-in) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_reference_file" type="data" format="featurexml,consensusxml,idxml" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/> + <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) <br>If '0', no explicit reference is set - the algorithm will select a reference"/> + <param name="param_algorithm_peptide_score_threshold" type="float" value="0.0" label="Score threshold for peptide hits to be used in the alignment" help="(-peptide_score_threshold) <br>Select a value that allows only 'high confidence' matches"/> + <param name="param_algorithm_min_run_occur" type="integer" min="2" optional="True" value="2" label="Minimum number of runs (incl" 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"/> + <param name="param_algorithm_max_rt_shift" type="float" min="0.0" optional="True" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" 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"/> + <param name="param_algorithm_use_unassigned_peptides" type="boolean" truevalue="-algorithm:use_unassigned_peptides" falsevalue="" checked="true" optional="True" label="Should unassigned peptide identifications be used when computing an alignment of feature maps?" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used"/> + <param name="param_algorithm_use_feature_rt" type="boolean" truevalue="-algorithm:use_feature_rt" falsevalue="" checked="false" optional="True" 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" 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'"/> + <param name="param_model_type" type="select" optional="True" value="b_spline" label="Type of model" help="(-type) "> + <option value="linear">linear</option> + <option value="b_spline">b_spline</option> + <option value="interpolated">interpolated</option> + </param> + <param name="param_model_linear_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression" falsevalue="" checked="false" optional="True" label="Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/> + <param name="param_model_b_spline_wavelength" type="float" min="0.0" optional="True" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" 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"/> + <param name="param_model_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for B-spline fitting" help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/> + <param name="param_model_b_spline_extrapolate" type="select" optional="True" value="linear" label="Method to use for extrapolation beyond the original data range" 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)"> + <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 name="param_model_b_spline_boundary_condition" type="integer" min="0" max="2" optional="True" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help="(-boundary_condition) "/> + <param name="param_model_interpolated_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) "> + <option value="linear">linear</option> + <option value="cspline">cspline</option> + <option value="akima">akima</option> + </param> + <expand macro="advanced_options"> + <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" metadata_source="param_in" format="input"/> + <data name="param_trafo_out" format="trafoxml"/> + </outputs> + <help>**What it does** + +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> + <expand macro="references"/> +</tool>