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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="2.0.0">
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3 <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MapAlignerIdentification</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>MapAlignerIdentification
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11
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12 -in
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13 #for token in $param_in:
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14 $token
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15 #end for
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16
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17 #if $rep_param_out:
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18 -out
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19 #for token in $rep_param_out:
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20 #if " " in str(token):
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21 "$token.param_out"
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22 #else
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23 $token.param_out
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24 #end if
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25 #end for
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26 #end if
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27
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28 #if $rep_param_trafo_out:
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29 -trafo_out
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30 #for token in $rep_param_trafo_out:
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31 #if " " in str(token):
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32 "$token.param_trafo_out"
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33 #else
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34 $token.param_trafo_out
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35 #end if
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36 #end for
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37 #end if
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38 -threads \${GALAXY_SLOTS:-24}
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39 #if $param_reference_file:
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40 -reference:file $param_reference_file
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41 #end if
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42 #if $param_reference_index:
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43 -reference:index $param_reference_index
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44 #end if
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45 #if $param_algorithm_peptide_score_threshold:
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46 -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold
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47 #end if
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48 #if $param_algorithm_min_run_occur:
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49 -algorithm:min_run_occur $param_algorithm_min_run_occur
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50 #end if
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51 #if $param_algorithm_max_rt_shift:
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52 -algorithm:max_rt_shift $param_algorithm_max_rt_shift
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53 #end if
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54 #if $param_algorithm_use_unassigned_peptides:
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55 -algorithm:use_unassigned_peptides
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56 #end if
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57 #if $param_algorithm_use_feature_rt:
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58 -algorithm:use_feature_rt
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59 #end if
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60 #if $param_model_type:
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61 -model:type
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62 #if " " in str($param_model_type):
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63 "$param_model_type"
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64 #else
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65 $param_model_type
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66 #end if
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67 #end if
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68 #if $param_model_linear_symmetric_regression:
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69 -model:linear:symmetric_regression
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70 #end if
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71 #if $param_model_b_spline_wavelength:
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72 -model:b_spline:wavelength $param_model_b_spline_wavelength
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73 #end if
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74 #if $param_model_b_spline_num_nodes:
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75 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
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76 #end if
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77 #if $param_model_b_spline_extrapolate:
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78 -model:b_spline:extrapolate
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79 #if " " in str($param_model_b_spline_extrapolate):
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80 "$param_model_b_spline_extrapolate"
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81 #else
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82 $param_model_b_spline_extrapolate
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83 #end if
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84 #end if
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85 #if $param_model_b_spline_boundary_condition:
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86 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
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87 #end if
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88 #if $param_model_interpolated_interpolation_type:
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89 -model:interpolated:interpolation_type
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90 #if " " in str($param_model_interpolated_interpolation_type):
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91 "$param_model_interpolated_interpolation_type"
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92 #else
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93 $param_model_interpolated_interpolation_type
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94 #end if
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95 #end if
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96 #if $adv_opts.adv_opts_selector=='advanced':
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97 #if $adv_opts.param_force:
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98 -force
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99 #end if
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100 #end if
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101 </command>
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102 <inputs>
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103 <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) ">
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104 <sanitizer>
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105 <valid initial="string.printable">
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106 <remove value="'"/>
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107 <remove value="""/>
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108 </valid>
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109 </sanitizer>
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110 </param>
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111 <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) "/>
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112 <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"/>
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113 <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"/>
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114 <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"/>
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115 <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"/>
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116 <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"/>
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117 <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'"/>
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118 <param name="param_model_type" type="select" optional="True" value="b_spline" label="Type of model" help="(-type) ">
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119 <option value="linear">linear</option>
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120 <option value="b_spline">b_spline</option>
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121 <option value="interpolated">interpolated</option>
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122 </param>
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123 <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'"/>
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124 <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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125 <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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126 <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)">
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127 <option value="linear">linear</option>
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128 <option value="b_spline">b_spline</option>
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129 <option value="constant">constant</option>
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130 <option value="global_linear">global_linear</option>
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131 </param>
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132 <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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133 <param name="param_model_interpolated_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) ">
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134 <option value="linear">linear</option>
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135 <option value="cspline">cspline</option>
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136 <option value="akima">akima</option>
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137 </param>
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138 <expand macro="advanced_options">
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139 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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140 </expand>
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141 </inputs>
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142 <outputs>
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143 <data name="param_out" metadata_source="param_in" format="input"/>
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144 <data name="param_trafo_out" format="trafoxml"/>
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145 </outputs>
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146 <help>**What it does**
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147
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148 Corrects retention time distortions between maps based on common peptide identifications.
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149
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150
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151 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help>
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152 <expand macro="references"/>
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153 </tool>
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