Mercurial > repos > galaxyp > openms_mapaligneridentification

annotate MapAlignerIdentification.xml @ 0:83983906eb4b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:43:49 -0500
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children 1f0a9c3cb526
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83983906eb4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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="MapAlignerIdentification" name="MapAlignerIdentification" version="2.3.0">
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5 <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MapAlignerIdentification</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>MapAlignerIdentification
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14
83983906eb4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19
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20 #if $rep_param_out:
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21 -out
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22 #for token in $rep_param_out:
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23 #if " " in str(token):
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24 "$token.param_out"
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25 #else
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26 $token.param_out
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27 #end if
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28 #end for
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29 #end if
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30
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31 #if $rep_param_trafo_out:
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32 -trafo_out
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33 #for token in $rep_param_trafo_out:
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34 #if " " in str(token):
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35 "$token.param_trafo_out"
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36 #else
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37 $token.param_trafo_out
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38 #end if
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39 #end for
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40 #end if
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41 #if $param_design:
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42 -design $param_design
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43 #end if
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44 #if $param_reference_file:
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45 -reference:file $param_reference_file
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46 #end if
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47 #if $param_reference_index:
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48 -reference:index $param_reference_index
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49 #end if
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50 #if $param_algorithm_min_run_occur:
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51 -algorithm:min_run_occur $param_algorithm_min_run_occur
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52 #end if
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53 #if $param_algorithm_max_rt_shift:
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54 -algorithm:max_rt_shift $param_algorithm_max_rt_shift
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55 #end if
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56 #if $param_algorithm_use_unassigned_peptides:
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57 -algorithm:use_unassigned_peptides
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58 #if " " in str($param_algorithm_use_unassigned_peptides):
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59 "$param_algorithm_use_unassigned_peptides"
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60 #else
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61 $param_algorithm_use_unassigned_peptides
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62 #end if
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63 #end if
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64 #if $param_algorithm_use_feature_rt:
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65 -algorithm:use_feature_rt
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66 #end if
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67 #if $param_model_type:
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68 -model:type
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69 #if " " in str($param_model_type):
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70 "$param_model_type"
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71 #else
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72 $param_model_type
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73 #end if
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74 #end if
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75 #if $param_model_linear_symmetric_regression:
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76 -model:linear:symmetric_regression
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77 #end if
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78 #if $param_model_b_spline_wavelength:
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79 -model:b_spline:wavelength $param_model_b_spline_wavelength
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80 #end if
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81 #if $param_model_b_spline_num_nodes:
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82 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
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83 #end if
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84 #if $param_model_b_spline_extrapolate:
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85 -model:b_spline:extrapolate
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86 #if " " in str($param_model_b_spline_extrapolate):
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87 "$param_model_b_spline_extrapolate"
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88 #else
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89 $param_model_b_spline_extrapolate
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90 #end if
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91 #end if
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92 #if $param_model_b_spline_boundary_condition:
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93 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
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94 #end if
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95 #if $param_model_lowess_span:
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96 -model:lowess:span $param_model_lowess_span
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97 #end if
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98 #if $param_model_lowess_num_iterations:
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99 -model:lowess:num_iterations $param_model_lowess_num_iterations
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100 #end if
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101 #if $param_model_lowess_delta:
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102 -model:lowess:delta $param_model_lowess_delta
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103 #end if
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104 #if $param_model_lowess_interpolation_type:
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105 -model:lowess:interpolation_type
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106 #if " " in str($param_model_lowess_interpolation_type):
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107 "$param_model_lowess_interpolation_type"
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108 #else
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109 $param_model_lowess_interpolation_type
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110 #end if
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111 #end if
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112 #if $param_model_lowess_extrapolation_type:
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113 -model:lowess:extrapolation_type
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114 #if " " in str($param_model_lowess_extrapolation_type):
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115 "$param_model_lowess_extrapolation_type"
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116 #else
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117 $param_model_lowess_extrapolation_type
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118 #end if
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119 #end if
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120 #if $param_model_interpolated_interpolation_type:
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121 -model:interpolated:interpolation_type
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122 #if " " in str($param_model_interpolated_interpolation_type):
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123 "$param_model_interpolated_interpolation_type"
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124 #else
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125 $param_model_interpolated_interpolation_type
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126 #end if
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127 #end if
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128 #if $param_model_interpolated_extrapolation_type:
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129 -model:interpolated:extrapolation_type
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130 #if " " in str($param_model_interpolated_extrapolation_type):
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131 "$param_model_interpolated_extrapolation_type"
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132 #else
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133 $param_model_interpolated_extrapolation_type
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134 #end if
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135 #end if
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136 #if $adv_opts.adv_opts_selector=='advanced':
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137 #if $adv_opts.param_force:
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138 -force
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139 #end if
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140 #end if
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141 </command>
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142 <inputs>
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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) ">
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144 <sanitizer>
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145 <valid initial="string.printable">
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146 <remove value="'"/>
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147 <remove value="&quot;"/>
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148 </valid>
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149 </sanitizer>
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150 </param>
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151 <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
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152 <param name="param_reference_file" type="data" format="featurexml,consensusxml,idxml" optional="True" label="File to use as reference" help="(-file) "/>
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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) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
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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. &lt;br&gt;Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
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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. &lt;br&gt;If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
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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">
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157 <option value="true" selected="true">true</option>
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158 <option value="false">false</option>
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159 </param>
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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. &lt;br&gt;Precludes 'use_unassigned_peptides'"/>
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161 <param name="param_model_type" display="radio" type="select" optional="False" value="b_spline" label="Type of model" help="(-type) ">
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162 <option value="linear">linear</option>
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163 <option value="b_spline" selected="true">b_spline</option>
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164 <option value="lowess">lowess</option>
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165 <option value="interpolated">interpolated</option>
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166 </param>
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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'"/>
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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"/>
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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"/>
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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)">
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171 <option value="linear" selected="true">linear</option>
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172 <option value="b_spline">b_spline</option>
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173 <option value="constant">constant</option>
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174 <option value="global_linear">global_linear</option>
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175 </param>
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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) "/>
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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"/>
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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) "/>
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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"/>
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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">
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181 <option value="linear">linear</option>
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182 <option value="cspline" selected="true">cspline</option>
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183 <option value="akima">akima</option>
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184 </param>
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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">
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186 <option value="two-point-linear">two-point-linear</option>
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187 <option value="four-point-linear" selected="true">four-point-linear</option>
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188 <option value="global-linear">global-linear</option>
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189 </param>
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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) ">
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191 <option value="linear">linear</option>
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192 <option value="cspline" selected="true">cspline</option>
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193 <option value="akima">akima</option>
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194 </param>
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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">
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196 <option value="two-point-linear" selected="true">two-point-linear</option>
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197 <option value="four-point-linear">four-point-linear</option>
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198 <option value="global-linear">global-linear</option>
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199 </param>
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200 <expand macro="advanced_options">
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201 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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202 </expand>
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203 </inputs>
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204 <outputs>
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205 <data name="param_out" metadata_source="param_in" format="input"/>
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206 <data name="param_trafo_out" format="trafoxml"/>
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207 </outputs>
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208 <help>Corrects retention time distortions between maps based on common peptide identifications.
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209
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210
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211 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help>
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212 </tool>