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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MapAlignerSpectrum" name="MapAlignerSpectrum" version="2.0.0">
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3 <description>Corrects retention time distortions between maps by spectrum alignment.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MapAlignerSpectrum</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>MapAlignerSpectrum
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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_algorithm_gapcost:
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40 -algorithm:gapcost $param_algorithm_gapcost
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41 #end if
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42 #if $param_algorithm_affinegapcost:
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43 -algorithm:affinegapcost $param_algorithm_affinegapcost
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44 #end if
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45 #if $param_algorithm_scorefunction:
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46 -algorithm:scorefunction
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47 #if " " in str($param_algorithm_scorefunction):
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48 "$param_algorithm_scorefunction"
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49 #else
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50 $param_algorithm_scorefunction
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51 #end if
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52 #end if
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53 #if $param_model_type:
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54 -model:type
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55 #if " " in str($param_model_type):
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56 "$param_model_type"
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57 #else
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58 $param_model_type
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59 #end if
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60 #end if
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61 #if $param_model_linear_symmetric_regression:
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62 -model:linear:symmetric_regression
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63 #end if
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64 #if $param_model_b_spline_wavelength:
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65 -model:b_spline:wavelength $param_model_b_spline_wavelength
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66 #end if
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67 #if $param_model_b_spline_num_nodes:
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68 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
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69 #end if
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70 #if $param_model_b_spline_extrapolate:
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71 -model:b_spline:extrapolate
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72 #if " " in str($param_model_b_spline_extrapolate):
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73 "$param_model_b_spline_extrapolate"
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74 #else
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75 $param_model_b_spline_extrapolate
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76 #end if
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77 #end if
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78 #if $param_model_b_spline_boundary_condition:
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79 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
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80 #end if
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81 #if $param_model_interpolated_interpolation_type:
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82 -model:interpolated:interpolation_type
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83 #if " " in str($param_model_interpolated_interpolation_type):
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84 "$param_model_interpolated_interpolation_type"
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85 #else
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86 $param_model_interpolated_interpolation_type
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87 #end if
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88 #end if
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89 #if $adv_opts.adv_opts_selector=='advanced':
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90 #if $adv_opts.param_force:
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91 -force
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92 #end if
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93 #if $adv_opts.param_algorithm_cutoff_score:
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94 -algorithm:cutoff_score $adv_opts.param_algorithm_cutoff_score
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95 #end if
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96 #if $adv_opts.param_algorithm_bucketsize:
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97 -algorithm:bucketsize $adv_opts.param_algorithm_bucketsize
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98 #end if
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99 #if $adv_opts.param_algorithm_anchorpoints:
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100 -algorithm:anchorpoints $adv_opts.param_algorithm_anchorpoints
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101 #end if
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102 #if $adv_opts.param_algorithm_mismatchscore:
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103 -algorithm:mismatchscore $adv_opts.param_algorithm_mismatchscore
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104 #end if
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105 #end if
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106 </command>
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107 <inputs>
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108 <param name="param_in" type="data" format="mzml" 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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109 <sanitizer>
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110 <valid initial="string.printable">
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111 <remove value="'"/>
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112 <remove value="""/>
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113 </valid>
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114 </sanitizer>
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115 </param>
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116 <param name="param_algorithm_gapcost" type="float" min="0.0" optional="True" value="1.0" label=" This Parameter stands for the cost of opining a gap in the Alignment" help="(-gapcost) A Gap means that one Spectrum can not be aligned directly to another Spectrum in the Map. This happens, when the similarity of both spectra a too low or even not present. Imagen as a insert or delete of the spectrum in the map. The gap is necessary for aligning, if we open a gap there is a possibility that an another spectrum can be correct aligned with a higher score as before without gap. But to open a gap is a negative event and has to be punished a bit, so such only in case it 's a good choice to open a gap, if the score is bad enough. The Parameter is to giving as a positive number, the implementation convert it to a negative number"/>
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117 <param name="param_algorithm_affinegapcost" type="float" min="0.0" optional="True" value="0.5" label=" This Parameter controls the cost of extension a already open gap" help="(-affinegapcost) The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure gap match gap match. There for the punishment for the extension of a gap has to be lower than the normal gapcost. If the the result of the alignment show high compression, it is a good idea to lower the affine gapcost or the normal gapcost"/>
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118 <param name="param_algorithm_scorefunction" type="select" optional="True" value="SteinScottImproveScore" label=" The score function is the core of an alignment" help="(-scorefunction) The success of an alignment depends mostly of the elected score function. The score function return the similarity of two Spectrum back. The score influence defines later the way of possible traceback. There exist many way of algorithm to calculate the score">
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119 <option value="SteinScottImproveScore">SteinScottImproveScore</option>
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120 <option value="ZhangSimilarityScore">ZhangSimilarityScore</option>
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121 </param>
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122 <param name="param_model_type" type="select" optional="True" value="interpolated" label="Type of model" help="(-type) ">
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123 <option value="linear">linear</option>
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124 <option value="b_spline">b_spline</option>
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125 <option value="interpolated">interpolated</option>
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126 </param>
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127 <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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128 <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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129 <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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130 <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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131 <option value="linear">linear</option>
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132 <option value="b_spline">b_spline</option>
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133 <option value="constant">constant</option>
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134 <option value="global_linear">global_linear</option>
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135 </param>
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136 <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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137 <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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138 <option value="linear">linear</option>
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139 <option value="cspline">cspline</option>
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140 <option value="akima">akima</option>
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141 </param>
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142 <expand macro="advanced_options">
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143 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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144 <param name="param_algorithm_cutoff_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="The Parameter defines the threshold which filtered Spectra, these Spectra are high potential candidate for deciding the interval of a sub-alignment" help="(-cutoff_score) Only those pair of Spectra are selected, which has a score higher or same of the threshold"/>
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145 <param name="param_algorithm_bucketsize" type="integer" min="1" optional="True" value="100" label="Defines the numbers of buckets" help="(-bucketsize) It is a quantize of the interval of those points, which defines the main alignment(match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve"/>
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146 <param name="param_algorithm_anchorpoints" type="integer" min="1" max="100" optional="True" value="100" label="Defines the percent of numbers of match points which a selected from one bucket" help="(-anchorpoints) The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve"/>
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147 <param name="param_algorithm_mismatchscore" type="float" max="0.0" optional="True" value="-5.0" label="Defines the score of two Spectra if they have no similarity to each othe" help="(-mismatchscore) "/>
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148 </expand>
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149 </inputs>
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150 <outputs>
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151 <data name="param_out" format="mzml"/>
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152 <data name="param_trafo_out" format="trafoxml"/>
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153 </outputs>
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154 <help>**What it does**
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155
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156 Corrects retention time distortions between maps by spectrum alignment.
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157
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158
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159 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerSpectrum.html</help>
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160 <expand macro="references"/>
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161 </tool>
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