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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.0.0">
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3 <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MapAlignerPoseClustering</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>MapAlignerPoseClustering
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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_max_num_peaks_considered:
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46 -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered
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47 #end if
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48 #if $param_algorithm_superimposer_mz_pair_max_distance:
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49 -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance
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50 #end if
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51 #if $param_algorithm_superimposer_num_used_points:
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52 -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points
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53 #end if
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54 #if $param_algorithm_superimposer_scaling_bucket_size:
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55 -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size
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56 #end if
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57 #if $param_algorithm_superimposer_shift_bucket_size:
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58 -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size
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59 #end if
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60 #if $param_algorithm_pairfinder_second_nearest_gap:
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61 -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap
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62 #end if
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63 #if $param_algorithm_pairfinder_use_identifications:
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64 -algorithm:pairfinder:use_identifications
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65 #end if
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66 #if $param_algorithm_pairfinder_ignore_charge:
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67 -algorithm:pairfinder:ignore_charge
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68 #end if
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69 #if $param_algorithm_pairfinder_distance_RT_max_difference:
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70 -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference
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71 #end if
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72 #if $param_algorithm_pairfinder_distance_MZ_max_difference:
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73 -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference
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74 #end if
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75 #if $param_algorithm_pairfinder_distance_MZ_unit:
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76 -algorithm:pairfinder:distance_MZ:unit
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77 #if " " in str($param_algorithm_pairfinder_distance_MZ_unit):
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78 "$param_algorithm_pairfinder_distance_MZ_unit"
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79 #else
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80 $param_algorithm_pairfinder_distance_MZ_unit
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81 #end if
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82 #end if
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83 #if $adv_opts.adv_opts_selector=='advanced':
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84 #if $adv_opts.param_force:
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85 -force
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86 #end if
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87 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
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88 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
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89 #end if
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90 #if $adv_opts.param_algorithm_superimposer_max_shift:
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91 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift
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92 #end if
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93 #if $adv_opts.param_algorithm_superimposer_max_scaling:
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94 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
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95 #end if
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96 #if $adv_opts.param_algorithm_superimposer_dump_buckets:
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97 -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets"
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98 #end if
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99 #if $adv_opts.param_algorithm_superimposer_dump_pairs:
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100 -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs"
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101 #end if
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102 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
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103 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
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104 #end if
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105 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
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106 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight
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107 #end if
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108 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent:
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109 -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent
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110 #end if
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111 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight:
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112 -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight
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113 #end if
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114 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent:
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115 -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent
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116 #end if
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117 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight:
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118 -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight
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119 #end if
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120 #end if
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121 </command>
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122 <inputs>
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123 <param name="param_in" type="data" format="featurexml,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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124 <sanitizer>
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125 <valid initial="string.printable">
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126 <remove value="'"/>
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127 <remove value="""/>
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128 </valid>
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129 </sanitizer>
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130 </param>
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131 <param name="param_reference_file" type="data" format="featurexml,mzml" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/>
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132 <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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133 <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/>
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134 <param name="param_algorithm_superimposer_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="(-mz_pair_max_distance) This condition applies to the pairs considered in hashing"/>
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135 <param name="param_algorithm_superimposer_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="(-num_used_points) Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1"/>
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136 <param name="param_algorithm_superimposer_scaling_bucket_size" type="float" min="0.0" optional="True" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="(-scaling_bucket_size) A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
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137 <param name="param_algorithm_superimposer_shift_bucket_size" type="float" min="0.0" optional="True" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="(-shift_bucket_size) A good choice for this would be about the time between consecutive MS scans"/>
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138 <param name="param_algorithm_pairfinder_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself" help="(-second_nearest_gap) "/>
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139 <param name="param_algorithm_pairfinder_use_identifications" type="boolean" truevalue="-algorithm:pairfinder:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help="(-use_identifications) "/>
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140 <param name="param_algorithm_pairfinder_ignore_charge" type="boolean" truevalue="-algorithm:pairfinder:ignore_charge" falsevalue="" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge) "/>
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141 <param name="param_algorithm_pairfinder_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference) "/>
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142 <param name="param_algorithm_pairfinder_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference) "/>
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143 <param name="param_algorithm_pairfinder_distance_MZ_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
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144 <option value="Da">Da</option>
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145 <option value="ppm">ppm</option>
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146 </param>
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147 <expand macro="advanced_options">
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148 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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149 <param name="param_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction) "/>
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150 <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming" help="(-max_shift) This applies for both directions"/>
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151 <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling) The minimal scaling is the reciprocal of this"/>
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152 <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets) A serial number for each invocation will be appended automatically">
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153 <sanitizer>
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154 <valid initial="string.printable">
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155 <remove value="'"/>
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156 <remove value="""/>
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157 </valid>
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158 </sanitizer>
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159 </param>
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160 <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs) A serial number for each invocation will be appended automatically">
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161 <sanitizer>
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162 <valid initial="string.printable">
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163 <remove value="'"/>
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164 <remove value="""/>
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165 </valid>
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166 </sanitizer>
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167 </param>
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168 <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
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169 <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this facto" help="(-weight) "/>
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170 <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
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171 <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this facto" help="(-weight) "/>
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172 <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
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173 <param name="param_algorithm_pairfinder_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this facto" help="(-weight) "/>
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174 </expand>
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175 </inputs>
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176 <outputs>
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177 <data name="param_out" metadata_source="param_in" format="input"/>
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178 <data name="param_trafo_out" format="trafoxml"/>
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179 </outputs>
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180 <help>**What it does**
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181
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182 Corrects retention time distortions between maps using a pose clustering approach.
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183
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184
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185 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help>
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186 <expand macro="references"/>
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187 </tool>
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