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

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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="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.0.0">
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5 <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MapAlignerPoseClustering</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>MapAlignerPoseClustering
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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
0
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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_max_num_peaks_considered:
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49 -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered
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50 #end if
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51 #if $param_algorithm_superimposer_mz_pair_max_distance:
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52 -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance
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53 #end if
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54 #if $param_algorithm_superimposer_num_used_points:
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55 -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points
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56 #end if
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57 #if $param_algorithm_superimposer_scaling_bucket_size:
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58 -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size
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59 #end if
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60 #if $param_algorithm_superimposer_shift_bucket_size:
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61 -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size
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62 #end if
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63 #if $param_algorithm_pairfinder_second_nearest_gap:
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64 -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap
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65 #end if
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66 #if $param_algorithm_pairfinder_use_identifications:
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67 -algorithm:pairfinder:use_identifications
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68 #end if
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69 #if $param_algorithm_pairfinder_ignore_charge:
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70 -algorithm:pairfinder:ignore_charge
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71 #end if
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72 #if $param_algorithm_pairfinder_distance_RT_max_difference:
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73 -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference
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74 #end if
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75 #if $param_algorithm_pairfinder_distance_MZ_max_difference:
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76 -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference
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77 #end if
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78 #if $param_algorithm_pairfinder_distance_MZ_unit:
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79 -algorithm:pairfinder:distance_MZ:unit
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80 #if &quot; &quot; in str($param_algorithm_pairfinder_distance_MZ_unit):
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81 &quot;$param_algorithm_pairfinder_distance_MZ_unit&quot;
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82 #else
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83 $param_algorithm_pairfinder_distance_MZ_unit
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84 #end if
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85 #end if
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86 #if $adv_opts.adv_opts_selector=='advanced':
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87 #if $adv_opts.param_force:
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88 -force
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89 #end if
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90 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
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91 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
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92 #end if
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93 #if $adv_opts.param_algorithm_superimposer_max_shift:
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94 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift
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95 #end if
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96 #if $adv_opts.param_algorithm_superimposer_max_scaling:
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97 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
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98 #end if
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99 #if $adv_opts.param_algorithm_superimposer_dump_buckets:
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100 -algorithm:superimposer:dump_buckets &quot;$adv_opts.param_algorithm_superimposer_dump_buckets&quot;
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101 #end if
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102 #if $adv_opts.param_algorithm_superimposer_dump_pairs:
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103 -algorithm:superimposer:dump_pairs &quot;$adv_opts.param_algorithm_superimposer_dump_pairs&quot;
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104 #end if
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105 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
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106 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
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107 #end if
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108 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
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109 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight
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110 #end if
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111 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent:
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112 -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent
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113 #end if
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114 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight:
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115 -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight
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116 #end if
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117 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent:
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118 -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent
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119 #end if
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120 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight:
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121 -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight
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122 #end if
0
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123 #end if
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124 </command>
4
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125 <inputs>
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126 <param format="xml,mzml" 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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127 <sanitizer>
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128 <valid initial="string.printable">
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129 <remove value="'"/>
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130 <remove value="&quot;"/>
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131 </valid>
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132 </sanitizer>
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133 </param>
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134 <param format="xml,mzml" help="(-file) " label="File to use as reference (same file format as input files required)" name="param_reference_file" optional="True" type="data"/>
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135 <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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136 <param help="(-max_num_peaks_considered) To use all, set to '-1'" label="The maximal number of peaks/features to be considered per map" min="-1" name="param_algorithm_max_num_peaks_considered" optional="True" type="integer" value="1000"/>
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137 <param help="(-mz_pair_max_distance) This condition applies to the pairs considered in hashing" label="Maximum of m/z deviation of corresponding elements in different maps" min="0.0" name="param_algorithm_superimposer_mz_pair_max_distance" optional="True" type="float" value="0.5"/>
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138 <param 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" label="Maximum number of elements considered in each map (selected by intensity)" min="-1" name="param_algorithm_superimposer_num_used_points" optional="True" type="integer" value="2000"/>
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139 <param help="(-scaling_bucket_size) A good choice for this would be a bit smaller than the error you would expect from repeated runs" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" min="0.0" name="param_algorithm_superimposer_scaling_bucket_size" optional="True" type="float" value="0.005"/>
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140 <param help="(-shift_bucket_size) A good choice for this would be about the time between consecutive MS scans" 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" min="0.0" name="param_algorithm_superimposer_shift_bucket_size" optional="True" type="float" value="3.0"/>
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141 <param help="(-second_nearest_gap) " label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" min="1.0" name="param_algorithm_pairfinder_second_nearest_gap" optional="True" type="float" value="2.0"/>
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142 <param checked="false" falsevalue="" help="(-use_identifications) " label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" name="param_algorithm_pairfinder_use_identifications" optional="True" truevalue="-algorithm:pairfinder:use_identifications" type="boolean"/>
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143 <param checked="false" falsevalue="" help="(-ignore_charge) " label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" name="param_algorithm_pairfinder_ignore_charge" optional="True" truevalue="-algorithm:pairfinder:ignore_charge" type="boolean"/>
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144 <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_pairfinder_distance_RT_max_difference" optional="True" type="float" value="100.0"/>
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145 <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_pairfinder_distance_MZ_max_difference" optional="True" type="float" value="0.3"/>
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146 <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_pairfinder_distance_MZ_unit" optional="True" type="select" value="Da">
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147 <option value="Da">Da</option>
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148 <option value="ppm">ppm</option>
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149 </param>
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150 <expand macro="advanced_options">
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151 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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152 <param help="(-rt_pair_distance_fraction) " 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)" max="1.0" min="0.0" name="param_algorithm_superimposer_rt_pair_distance_fraction" optional="True" type="float" value="0.1"/>
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153 <param help="(-max_shift) This applies for both directions" label="Maximal shift which is considered during histogramming (in seconds)" min="0.0" name="param_algorithm_superimposer_max_shift" optional="True" type="float" value="1000.0"/>
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154 <param help="(-max_scaling) The minimal scaling is the reciprocal of this" label="Maximal scaling which is considered during histogramming" min="1.0" name="param_algorithm_superimposer_max_scaling" optional="True" type="float" value="2.0"/>
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155 <param help="(-dump_buckets) A serial number for each invocation will be appended automatically" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" name="param_algorithm_superimposer_dump_buckets" size="30" type="text">
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156 <sanitizer>
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157 <valid initial="string.printable">
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158 <remove value="'"/>
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159 <remove value="&quot;"/>
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160 </valid>
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161 </sanitizer>
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162 </param>
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163 <param help="(-dump_pairs) A serial number for each invocation will be appended automatically" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" name="param_algorithm_superimposer_dump_pairs" size="30" type="text">
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164 <sanitizer>
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165 <valid initial="string.printable">
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166 <remove value="'"/>
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167 <remove value="&quot;"/>
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168 </valid>
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169 </sanitizer>
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170 </param>
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171 <param help="(-exponent) " label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_pairfinder_distance_RT_exponent" optional="True" type="float" value="1.0"/>
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172 <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_pairfinder_distance_RT_weight" optional="True" type="float" value="1.0"/>
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173 <param help="(-exponent) " label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_pairfinder_distance_MZ_exponent" optional="True" type="float" value="2.0"/>
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174 <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_pairfinder_distance_MZ_weight" optional="True" type="float" value="1.0"/>
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175 <param help="(-exponent) " label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_pairfinder_distance_intensity_exponent" optional="True" type="float" value="1.0"/>
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176 <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_pairfinder_distance_intensity_weight" optional="True" type="float" value="0.0"/>
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177 </expand>
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178 </inputs>
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179 <outputs>
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180 <data format="input" metadata_source="param_in" name="param_out"/>
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181 <data format="trafoxml" name="param_trafo_out"/>
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182 </outputs>
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183 <help>Corrects retention time distortions between maps using a pose clustering approach.
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184
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185
4
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186 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help>
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187 </tool>