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annotate MapRTTransformer.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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4
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Map Alignment]-->
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4 <tool id="MapRTTransformer" name="MapRTTransformer" version="2.0.0">
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5 <description>Applies retention time transformations to maps.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MapRTTransformer</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>MapRTTransformer
0
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_trafo_in:
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22 -trafo_in $param_trafo_in
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23 #end if
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24 #if $param_trafo_out:
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25 -trafo_out $param_trafo_out
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26 #end if
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27 #if $param_invert:
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28 -invert
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29 #end if
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30 #if $param_store_original_rt:
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31 -store_original_rt
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32 #end if
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33 -threads \${GALAXY_SLOTS:-24}
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34 #if $param_model_type:
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35 -model:type
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36 #if &quot; &quot; in str($param_model_type):
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37 &quot;$param_model_type&quot;
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38 #else
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39 $param_model_type
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40 #end if
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41 #end if
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42 #if $param_model_linear_symmetric_regression:
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43 -model:linear:symmetric_regression
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44 #end if
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45 #if $param_model_b_spline_wavelength:
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46 -model:b_spline:wavelength $param_model_b_spline_wavelength
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47 #end if
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48 #if $param_model_b_spline_num_nodes:
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49 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
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50 #end if
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51 #if $param_model_b_spline_extrapolate:
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52 -model:b_spline:extrapolate
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53 #if &quot; &quot; in str($param_model_b_spline_extrapolate):
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54 &quot;$param_model_b_spline_extrapolate&quot;
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55 #else
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56 $param_model_b_spline_extrapolate
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57 #end if
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58 #end if
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59 #if $param_model_b_spline_boundary_condition:
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60 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
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61 #end if
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62 #if $param_model_interpolated_interpolation_type:
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63 -model:interpolated:interpolation_type
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64 #if &quot; &quot; in str($param_model_interpolated_interpolation_type):
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65 &quot;$param_model_interpolated_interpolation_type&quot;
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66 #else
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67 $param_model_interpolated_interpolation_type
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68 #end if
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69 #end if
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70 #if $adv_opts.adv_opts_selector=='advanced':
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71 #if $adv_opts.param_force:
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72 -force
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73 #end if
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74 #end if
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75 </command>
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76 <inputs>
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77 <param format="xml,consensusxml,mzml" help="(-in) " label="Input file to transform (separated by blanks)" name="param_in" optional="True" type="data"/>
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78 <param format="trafoxml" help="(-trafo_in) " label="Transformation to apply" name="param_trafo_in" optional="False" type="data"/>
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79 <param checked="false" falsevalue="" help="(-invert) " label="Invert transformation (approximatively) before applying it" name="param_invert" optional="True" truevalue="-invert" type="boolean"/>
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80 <param checked="false" falsevalue="" help="(-store_original_rt) " label="Store the original retention times (before transformation) as meta data in the output file" name="param_store_original_rt" optional="True" truevalue="-store_original_rt" type="boolean"/>
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81 <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="none">
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82 <option value="none">none</option>
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83 <option value="linear">linear</option>
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84 <option value="b_spline">b_spline</option>
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85 <option value="interpolated">interpolated</option>
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86 </param>
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87 <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"/>
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88 <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"/>
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89 <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"/>
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90 <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">
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91 <option value="linear">linear</option>
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92 <option value="b_spline">b_spline</option>
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93 <option value="constant">constant</option>
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94 <option value="global_linear">global_linear</option>
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95 </param>
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96 <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"/>
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97 <param help="(-interpolation_type) " label="Type of interpolation to apply" name="param_model_interpolated_interpolation_type" optional="True" type="select" value="cspline">
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98 <option value="linear">linear</option>
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99 <option value="cspline">cspline</option>
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100 <option value="akima">akima</option>
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101 </param>
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102 <expand macro="advanced_options">
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103 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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104 </expand>
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105 </inputs>
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106 <outputs>
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107 <data format="input" metadata_source="param_in" name="param_out"/>
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108 <data format="trafoxml" name="param_trafo_out"/>
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109 </outputs>
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110 <help>Applies retention time transformations to maps.
0
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111
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112
4
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113 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html</help>
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114 </tool>