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

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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="MapAlignerIdentification" name="MapAlignerIdentification" version="2.0.0">
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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
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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 $rep_param_out:
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23 #if &quot; &quot; in str(token):
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24 &quot;$token.param_out&quot;
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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
4
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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 $rep_param_trafo_out:
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34 #if &quot; &quot; in str(token):
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35 &quot;$token.param_trafo_out&quot;
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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 -threads \${GALAXY_SLOTS:-24}
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42 #if $param_reference_file:
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43 -reference:file $param_reference_file
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44 #end if
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45 #if $param_reference_index:
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46 -reference:index $param_reference_index
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47 #end if
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48 #if $param_algorithm_peptide_score_threshold:
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49 -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold
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50 #end if
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51 #if $param_algorithm_min_run_occur:
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52 -algorithm:min_run_occur $param_algorithm_min_run_occur
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53 #end if
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54 #if $param_algorithm_max_rt_shift:
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55 -algorithm:max_rt_shift $param_algorithm_max_rt_shift
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56 #end if
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57 #if $param_algorithm_use_unassigned_peptides:
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58 -algorithm:use_unassigned_peptides
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59 #end if
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60 #if $param_algorithm_use_feature_rt:
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61 -algorithm:use_feature_rt
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62 #end if
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63 #if $param_model_type:
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64 -model:type
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65 #if &quot; &quot; in str($param_model_type):
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66 &quot;$param_model_type&quot;
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67 #else
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68 $param_model_type
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69 #end if
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70 #end if
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71 #if $param_model_linear_symmetric_regression:
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72 -model:linear:symmetric_regression
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73 #end if
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74 #if $param_model_b_spline_wavelength:
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75 -model:b_spline:wavelength $param_model_b_spline_wavelength
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76 #end if
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77 #if $param_model_b_spline_num_nodes:
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78 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
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79 #end if
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80 #if $param_model_b_spline_extrapolate:
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81 -model:b_spline:extrapolate
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82 #if &quot; &quot; in str($param_model_b_spline_extrapolate):
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83 &quot;$param_model_b_spline_extrapolate&quot;
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84 #else
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85 $param_model_b_spline_extrapolate
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86 #end if
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87 #end if
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88 #if $param_model_b_spline_boundary_condition:
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89 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
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90 #end if
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91 #if $param_model_interpolated_interpolation_type:
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92 -model:interpolated:interpolation_type
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93 #if &quot; &quot; in str($param_model_interpolated_interpolation_type):
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94 &quot;$param_model_interpolated_interpolation_type&quot;
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95 #else
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96 $param_model_interpolated_interpolation_type
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97 #end if
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98 #end if
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99 #if $adv_opts.adv_opts_selector=='advanced':
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100 #if $adv_opts.param_force:
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101 -force
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102 #end if
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103 #end if
0
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104 </command>
4
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105 <inputs>
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106 <param format="xml,consensusxml" help="(-in) " label="Input files to align (all must have the same file type)" multiple="true" name="param_in" optional="False" size="30" type="data">
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107 <sanitizer>
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108 <valid initial="string.printable">
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109 <remove value="'"/>
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110 <remove value="&quot;"/>
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111 </valid>
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112 </sanitizer>
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113 </param>
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114 <param format="xml,consensusxml" help="(-file) " label="File to use as reference" name="param_reference_file" optional="True" type="data"/>
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115 <param help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference" label="Use one of the input files as reference ('1' for the first file, etc.)" min="0" name="param_reference_index" optional="True" type="integer" value="0"/>
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116 <param help="(-peptide_score_threshold) &lt;br&gt;Select a value that allows only 'high confidence' matches" label="Score threshold for peptide hits to be used in the alignment" name="param_algorithm_peptide_score_threshold" type="float" value="0.0"/>
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117 <param help="(-min_run_occur) reference, if any) a peptide must occur in 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" label="Minimum number of runs (incl" min="2" name="param_algorithm_min_run_occur" optional="True" type="integer" value="2"/>
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118 <param 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" label="Maximum realistic RT difference for a peptide (median per run vs" min="0.0" name="param_algorithm_max_rt_shift" optional="True" type="float" value="0.5"/>
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119 <param checked="true" falsevalue="" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used" label="Should unassigned peptide identifications be used when computing an alignment of feature maps?" name="param_algorithm_use_unassigned_peptides" optional="True" truevalue="-algorithm:use_unassigned_peptides" type="boolean"/>
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120 <param checked="false" falsevalue="" 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'" 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" name="param_algorithm_use_feature_rt" optional="True" truevalue="-algorithm:use_feature_rt" type="boolean"/>
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121 <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="b_spline">
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122 <option value="linear">linear</option>
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123 <option value="b_spline">b_spline</option>
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124 <option value="interpolated">interpolated</option>
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125 </param>
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126 <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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127 <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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128 <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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129 <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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130 <option value="linear">linear</option>
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131 <option value="b_spline">b_spline</option>
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132 <option value="constant">constant</option>
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133 <option value="global_linear">global_linear</option>
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134 </param>
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135 <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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136 <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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137 <option value="linear">linear</option>
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138 <option value="cspline">cspline</option>
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139 <option value="akima">akima</option>
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140 </param>
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141 <expand macro="advanced_options">
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142 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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143 </expand>
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144 </inputs>
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145 <outputs>
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146 <data format="input" metadata_source="param_in" name="param_out"/>
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147 <data format="trafoxml" name="param_trafo_out"/>
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148 </outputs>
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149 <help>Corrects retention time distortions between maps based on common peptide identifications.
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150
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151
4
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152 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help>
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153 </tool>