Mercurial > repos > galaxyp > openms_maprttransformer

annotate MapRTTransformer.xml @ 9:fd6de4cdb9e9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:22:43 +0000
parents 0fc718253aab
children 88ac532206c7
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652ee76d7113 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Map Alignment]-->
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4 <tool id="MapRTTransformer" name="MapRTTransformer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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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 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 #if $in:
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20 mkdir in &&
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21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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22 #end if
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23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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24 mkdir out &&
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25 #end if
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26 mkdir trafo_in &&
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27 ln -s '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' &&
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28 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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29 mkdir trafo_out &&
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30 #end if
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32 ## Main program call
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34 set -o pipefail &&
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35 @EXECUTABLE@ -write_ctd ./ &&
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36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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38 #if $in:
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39 -in
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40 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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41 #end if
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42 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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43 -out
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44 'out/output.${in.ext}'
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45 #end if
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46 -trafo_in
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47 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)'
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48 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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49 -trafo_out
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50 'trafo_out/output.${gxy2omsext("trafoxml")}'
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51 #end if
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52 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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53 | tee '$stdout'
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54 #end if
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55
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56 ## Postprocessing
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57 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 && mv 'out/output.${in.ext}' '$out'
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59 #end if
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60 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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61 && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out'
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62 #end if
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63 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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64 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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65 #end if]]></command>
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66 <configfiles>
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67 <inputs name="args_json" data_style="paths"/>
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68 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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69 </configfiles>
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70 <inputs>
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71 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="true" label="Input file to transform (separated by blanks)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
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72 <param name="trafo_in" argument="-trafo_in" type="data" format="trafoxml" optional="false" label="Transformation to apply" help=" select trafoxml data sets(s)"/>
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73 <param name="invert" argument="-invert" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Invert transformation (approximatively) before applying it" help=""/>
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74 <param name="store_original_rt" argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output file" help=""/>
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75 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
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76 <param name="type" argument="-model:type" type="select" optional="false" label="Type of model" help="">
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77 <option value="none" selected="true">none</option>
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78 <option value="linear">linear</option>
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79 <option value="b_spline">b_spline</option>
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80 <option value="lowess">lowess</option>
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81 <option value="interpolated">interpolated</option>
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82 <expand macro="list_string_san"/>
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83 </param>
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84 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
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85 <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
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86 <param name="x_weight" argument="-model:linear:x_weight" display="radio" type="select" optional="true" label="Weight x values" help="">
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87 <option value="">default (nothing chosen)</option>
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88 <option value="1/x">1/x</option>
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89 <option value="1/x2">1/x2</option>
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90 <option value="ln(x)">ln(x)</option>
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91 <option value=""></option>
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92 <expand macro="list_string_san"/>
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93 </param>
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94 <param name="y_weight" argument="-model:linear:y_weight" display="radio" type="select" optional="true" label="Weight y values" help="">
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95 <option value="">default (nothing chosen)</option>
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96 <option value="1/y">1/y</option>
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97 <option value="1/y2">1/y2</option>
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98 <option value="ln(y)">ln(y)</option>
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99 <option value=""></option>
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100 <expand macro="list_string_san"/>
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101 </param>
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102 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
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103 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
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104 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
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105 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
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106 </section>
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107 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
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108 <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="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"/>
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109 <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
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110 <param name="extrapolate" argument="-model:b_spline:extrapolate" display="radio" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'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)">
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111 <option value="linear" selected="true">linear</option>
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112 <option value="b_spline">b_spline</option>
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113 <option value="constant">constant</option>
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114 <option value="global_linear">global_linear</option>
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115 <expand macro="list_string_san"/>
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116 </param>
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117 <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
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118 </section>
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119 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
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120 <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
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121 <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
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122 <param name="delta" argument="-model:lowess:delta" type="float" optional="true" 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="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"/>
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123 <param name="interpolation_type" argument="-model:lowess:interpolation_type" display="radio" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
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124 <option value="linear">linear</option>
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125 <option value="cspline" selected="true">cspline</option>
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126 <option value="akima">akima</option>
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127 <expand macro="list_string_san"/>
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128 </param>
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129 <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" display="radio" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'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">
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130 <option value="two-point-linear">two-point-linear</option>
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131 <option value="four-point-linear" selected="true">four-point-linear</option>
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132 <option value="global-linear">global-linear</option>
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133 <expand macro="list_string_san"/>
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134 </param>
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135 </section>
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136 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
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137 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" display="radio" type="select" optional="false" label="Type of interpolation to apply" help="">
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138 <option value="linear">linear</option>
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139 <option value="cspline" selected="true">cspline</option>
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140 <option value="akima">akima</option>
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141 <expand macro="list_string_san"/>
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142 </param>
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143 <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" display="radio" type="select" optional="false" 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="Note that global-linear may not be continuous at the border">
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144 <option value="two-point-linear" selected="true">two-point-linear</option>
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145 <option value="four-point-linear">four-point-linear</option>
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146 <option value="global-linear">global-linear</option>
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147 <expand macro="list_string_san"/>
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148 </param>
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149 </section>
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150 </section>
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151 <expand macro="adv_opts_macro">
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152 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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153 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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154 <expand macro="list_string_san"/>
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155 </param>
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156 </expand>
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157 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
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158 <option value="out_FLAG">out (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)</option>
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159 <option value="trafo_out_FLAG">trafo_out (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)</option>
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160 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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161 </param>
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162 </inputs>
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163 <outputs>
9
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164 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in">
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165 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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166 </data>
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167 <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
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168 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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169 </data>
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170 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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171 <filter>OPTIONAL_OUTPUTS is None</filter>
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172 </data>
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173 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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174 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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175 </data>
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176 </outputs>
9
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177 <tests>
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178 <expand macro="autotest_MapRTTransformer"/>
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179 <expand macro="manutest_MapRTTransformer"/>
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180 </tests>
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181 <help><![CDATA[Applies retention time transformations to maps.
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182
652ee76d7113 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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183
9
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184 For more information, visit http://www.openms.de/documentation/TOPP_MapRTTransformer.html]]></help>
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185 <expand macro="references"/>
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186 </tool>