Mercurial > repos > galaxyp > openms_mapaligneridentification
comparison MapAlignerIdentification.xml @ 0:83983906eb4b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
| author | galaxyp |
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| date | Mon, 12 Feb 2018 13:43:49 -0500 |
| parents | |
| children | 1f0a9c3cb526 |
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| -1:000000000000 | 0:83983906eb4b |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | |
| 3 <!--Proposed Tool Section: [Map Alignment]--> | |
| 4 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="2.3.0"> | |
| 5 <description>Corrects retention time distortions between maps based on common peptide identifications.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">MapAlignerIdentification</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>MapAlignerIdentification | |
| 14 | |
| 15 -in | |
| 16 #for token in $param_in: | |
| 17 $token | |
| 18 #end for | |
| 19 | |
| 20 #if $rep_param_out: | |
| 21 -out | |
| 22 #for token in $rep_param_out: | |
| 23 #if " " in str(token): | |
| 24 "$token.param_out" | |
| 25 #else | |
| 26 $token.param_out | |
| 27 #end if | |
| 28 #end for | |
| 29 #end if | |
| 30 | |
| 31 #if $rep_param_trafo_out: | |
| 32 -trafo_out | |
| 33 #for token in $rep_param_trafo_out: | |
| 34 #if " " in str(token): | |
| 35 "$token.param_trafo_out" | |
| 36 #else | |
| 37 $token.param_trafo_out | |
| 38 #end if | |
| 39 #end for | |
| 40 #end if | |
| 41 #if $param_design: | |
| 42 -design $param_design | |
| 43 #end if | |
| 44 #if $param_reference_file: | |
| 45 -reference:file $param_reference_file | |
| 46 #end if | |
| 47 #if $param_reference_index: | |
| 48 -reference:index $param_reference_index | |
| 49 #end if | |
| 50 #if $param_algorithm_min_run_occur: | |
| 51 -algorithm:min_run_occur $param_algorithm_min_run_occur | |
| 52 #end if | |
| 53 #if $param_algorithm_max_rt_shift: | |
| 54 -algorithm:max_rt_shift $param_algorithm_max_rt_shift | |
| 55 #end if | |
| 56 #if $param_algorithm_use_unassigned_peptides: | |
| 57 -algorithm:use_unassigned_peptides | |
| 58 #if " " in str($param_algorithm_use_unassigned_peptides): | |
| 59 "$param_algorithm_use_unassigned_peptides" | |
| 60 #else | |
| 61 $param_algorithm_use_unassigned_peptides | |
| 62 #end if | |
| 63 #end if | |
| 64 #if $param_algorithm_use_feature_rt: | |
| 65 -algorithm:use_feature_rt | |
| 66 #end if | |
| 67 #if $param_model_type: | |
| 68 -model:type | |
| 69 #if " " in str($param_model_type): | |
| 70 "$param_model_type" | |
| 71 #else | |
| 72 $param_model_type | |
| 73 #end if | |
| 74 #end if | |
| 75 #if $param_model_linear_symmetric_regression: | |
| 76 -model:linear:symmetric_regression | |
| 77 #end if | |
| 78 #if $param_model_b_spline_wavelength: | |
| 79 -model:b_spline:wavelength $param_model_b_spline_wavelength | |
| 80 #end if | |
| 81 #if $param_model_b_spline_num_nodes: | |
| 82 -model:b_spline:num_nodes $param_model_b_spline_num_nodes | |
| 83 #end if | |
| 84 #if $param_model_b_spline_extrapolate: | |
| 85 -model:b_spline:extrapolate | |
| 86 #if " " in str($param_model_b_spline_extrapolate): | |
| 87 "$param_model_b_spline_extrapolate" | |
| 88 #else | |
| 89 $param_model_b_spline_extrapolate | |
| 90 #end if | |
| 91 #end if | |
| 92 #if $param_model_b_spline_boundary_condition: | |
| 93 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition | |
| 94 #end if | |
| 95 #if $param_model_lowess_span: | |
| 96 -model:lowess:span $param_model_lowess_span | |
| 97 #end if | |
| 98 #if $param_model_lowess_num_iterations: | |
| 99 -model:lowess:num_iterations $param_model_lowess_num_iterations | |
| 100 #end if | |
| 101 #if $param_model_lowess_delta: | |
| 102 -model:lowess:delta $param_model_lowess_delta | |
| 103 #end if | |
| 104 #if $param_model_lowess_interpolation_type: | |
| 105 -model:lowess:interpolation_type | |
| 106 #if " " in str($param_model_lowess_interpolation_type): | |
| 107 "$param_model_lowess_interpolation_type" | |
| 108 #else | |
| 109 $param_model_lowess_interpolation_type | |
| 110 #end if | |
| 111 #end if | |
| 112 #if $param_model_lowess_extrapolation_type: | |
| 113 -model:lowess:extrapolation_type | |
| 114 #if " " in str($param_model_lowess_extrapolation_type): | |
| 115 "$param_model_lowess_extrapolation_type" | |
| 116 #else | |
| 117 $param_model_lowess_extrapolation_type | |
| 118 #end if | |
| 119 #end if | |
| 120 #if $param_model_interpolated_interpolation_type: | |
| 121 -model:interpolated:interpolation_type | |
| 122 #if " " in str($param_model_interpolated_interpolation_type): | |
| 123 "$param_model_interpolated_interpolation_type" | |
| 124 #else | |
| 125 $param_model_interpolated_interpolation_type | |
| 126 #end if | |
| 127 #end if | |
| 128 #if $param_model_interpolated_extrapolation_type: | |
| 129 -model:interpolated:extrapolation_type | |
| 130 #if " " in str($param_model_interpolated_extrapolation_type): | |
| 131 "$param_model_interpolated_extrapolation_type" | |
| 132 #else | |
| 133 $param_model_interpolated_extrapolation_type | |
| 134 #end if | |
| 135 #end if | |
| 136 #if $adv_opts.adv_opts_selector=='advanced': | |
| 137 #if $adv_opts.param_force: | |
| 138 -force | |
| 139 #end if | |
| 140 #end if | |
| 141 </command> | |
| 142 <inputs> | |
| 143 <param name="param_in" type="data" format="featurexml,consensusxml,idxml" multiple="true" optional="False" size="30" label="Input files to align (all must have the same file type)" help="(-in) "> | |
| 144 <sanitizer> | |
| 145 <valid initial="string.printable"> | |
| 146 <remove value="'"/> | |
| 147 <remove value="""/> | |
| 148 </valid> | |
| 149 </sanitizer> | |
| 150 </param> | |
| 151 <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/> | |
| 152 <param name="param_reference_file" type="data" format="featurexml,consensusxml,idxml" optional="True" label="File to use as reference" help="(-file) "/> | |
| 153 <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"/> | |
| 154 <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) in which a peptide must occur to be used for the alignment. <br>Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/> | |
| 155 <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"/> | |
| 156 <param name="param_algorithm_use_unassigned_peptides" display="radio" type="select" optional="False" value="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps?" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used"> | |
| 157 <option value="true" selected="true">true</option> | |
| 158 <option value="false">false</option> | |
| 159 </param> | |
| 160 <param name="param_algorithm_use_feature_rt" display="radio" type="boolean" truevalue="-algorithm:use_feature_rt" falsevalue="" checked="false" optional="True" label="When aligning feature or consensus 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'"/> | |
| 161 <param name="param_model_type" display="radio" type="select" optional="False" value="b_spline" label="Type of model" help="(-type) "> | |
| 162 <option value="linear">linear</option> | |
| 163 <option value="b_spline" selected="true">b_spline</option> | |
| 164 <option value="lowess">lowess</option> | |
| 165 <option value="interpolated">interpolated</option> | |
| 166 </param> | |
| 167 <param name="param_model_linear_symmetric_regression" display="radio" 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'"/> | |
| 168 <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"/> | |
| 169 <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"/> | |
| 170 <param name="param_model_b_spline_extrapolate" display="radio" type="select" optional="False" 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)"> | |
| 171 <option value="linear" selected="true">linear</option> | |
| 172 <option value="b_spline">b_spline</option> | |
| 173 <option value="constant">constant</option> | |
| 174 <option value="global_linear">global_linear</option> | |
| 175 </param> | |
| 176 <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) "/> | |
| 177 <param name="param_model_lowess_span" type="float" min="0.0" max="1.0" optional="True" value="0.666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="(-span) Choosing this parameter in the range .2 to .8 usually results in a good fit"/> | |
| 178 <param name="param_model_lowess_num_iterations" type="integer" min="0" optional="True" value="3" label="Number of robustifying iterations for lowess fitting" help="(-num_iterations) "/> | |
| 179 <param name="param_model_lowess_delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input," help="(-delta) e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/> | |
| 180 <param name="param_model_lowess_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Method to use for interpolation between datapoints computed by lowess" help="(-interpolation_type) 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation"> | |
| 181 <option value="linear">linear</option> | |
| 182 <option value="cspline" selected="true">cspline</option> | |
| 183 <option value="akima">akima</option> | |
| 184 </param> | |
| 185 <param name="param_model_lowess_extrapolation_type" display="radio" type="select" optional="False" value="four-point-linear" label="Method to use for extrapolation outside the data range" help="(-extrapolation_type) 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation"> | |
| 186 <option value="two-point-linear">two-point-linear</option> | |
| 187 <option value="four-point-linear" selected="true">four-point-linear</option> | |
| 188 <option value="global-linear">global-linear</option> | |
| 189 </param> | |
| 190 <param name="param_model_interpolated_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) "> | |
| 191 <option value="linear">linear</option> | |
| 192 <option value="cspline" selected="true">cspline</option> | |
| 193 <option value="akima">akima</option> | |
| 194 </param> | |
| 195 <param name="param_model_interpolated_extrapolation_type" display="radio" type="select" optional="False" value="two-point-linear" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="(-extrapolation_type) Note that global-linear may not be continuous at the border"> | |
| 196 <option value="two-point-linear" selected="true">two-point-linear</option> | |
| 197 <option value="four-point-linear">four-point-linear</option> | |
| 198 <option value="global-linear">global-linear</option> | |
| 199 </param> | |
| 200 <expand macro="advanced_options"> | |
| 201 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 202 </expand> | |
| 203 </inputs> | |
| 204 <outputs> | |
| 205 <data name="param_out" metadata_source="param_in" format="input"/> | |
| 206 <data name="param_trafo_out" format="trafoxml"/> | |
| 207 </outputs> | |
| 208 <help>Corrects retention time distortions between maps based on common peptide identifications. | |
| 209 | |
| 210 | |
| 211 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help> | |
| 212 </tool> |