Mercurial > repos > galaxyp > openms_mapalignerposeclustering

annotate MapAlignerPoseClustering.xml @ 1:40ca4302e603 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
author galaxyp
date Mon, 12 Feb 2018 10:28:56 -0500
parents 70f729e59244
children 304c13ce9577
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70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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1 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.2.0">
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2 <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="stdio"/>
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8 <expand macro="requirements"/>
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9 <command><![CDATA[
1
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11 mkdir -p ./results_trafoxml ./results_out &&
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12 MapAlignerPoseClustering
1
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40ca4302e603 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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14 -in
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15 #for $infile in $param_in:
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16 '$infile'
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17 #end for
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19 -out
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20 #for $counter,$infile in enumerate($param_in):
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21 ./results_out/${infile.element_identifier}.${infile.extension}
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22 #end for
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23
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24 -trafo_out
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25 #for $counter,$infile in enumerate($param_in):
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26 ./results_trafoxml/${infile.element_identifier}.trafoxml
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27 #end for
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29 -threads "\${GALAXY_SLOTS:-1}"
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31 #if $param_reference_file:
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32 -reference:file $param_reference_file
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33 #end if
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34 #if $param_reference_index:
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35 -reference:index $param_reference_index
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36 #end if
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37 #if $param_algorithm_max_num_peaks_considered:
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38 -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered
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39 #end if
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40 #if $param_algorithm_superimposer_mz_pair_max_distance:
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41 -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance
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42 #end if
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43 #if $param_algorithm_superimposer_num_used_points:
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44 -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points
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45 #end if
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46 #if $param_algorithm_superimposer_scaling_bucket_size:
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47 -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size
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48 #end if
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49 #if $param_algorithm_superimposer_shift_bucket_size:
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50 -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size
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51 #end if
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52 #if $param_algorithm_pairfinder_second_nearest_gap:
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53 -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap
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54 #end if
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55 #if $param_algorithm_pairfinder_use_identifications:
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56 -algorithm:pairfinder:use_identifications
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57 #end if
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58 #if $param_algorithm_pairfinder_ignore_charge:
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59 -algorithm:pairfinder:ignore_charge
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60 #end if
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61 #if $param_algorithm_pairfinder_distance_RT_max_difference:
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62 -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference
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63 #end if
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64 #if $param_algorithm_pairfinder_distance_MZ_max_difference:
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65 -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference
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66 #end if
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67 #if $param_algorithm_pairfinder_distance_MZ_unit:
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68 -algorithm:pairfinder:distance_MZ:unit
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69 #if " " in str($param_algorithm_pairfinder_distance_MZ_unit):
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70 "$param_algorithm_pairfinder_distance_MZ_unit"
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71 #else
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72 $param_algorithm_pairfinder_distance_MZ_unit
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73 #end if
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74 #end if
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75 #if $adv_opts.adv_opts_selector=='advanced':
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76
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77 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
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78 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
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79 #end if
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80 #if $adv_opts.param_algorithm_superimposer_max_shift:
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81 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift
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82 #end if
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83 #if $adv_opts.param_algorithm_superimposer_max_scaling:
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84 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
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85 #end if
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86
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87 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
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88 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
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89 #end if
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90 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
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91 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight
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92 #end if
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93 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent:
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94 -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent
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95 #end if
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96 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight:
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97 -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight
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98 #end if
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99 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent:
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100 -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent
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101 #end if
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102 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight:
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103 -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight
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104 #end if
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105 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform:
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106 -algorithm:pairfinder:distance_intensity:log_transform
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107 #if " " in str($adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform):
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108 "$adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform"
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109 #else
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110 $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform
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111 #end if
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112 #end if
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113 #end if
1
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114
0
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115 ]]>
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116 </command>
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117 <inputs>
1
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118 <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/>
0
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119 <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/>
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120 <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) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
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121 <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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122 <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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123 <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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124 <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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125 <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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126 <param name="param_algorithm_pairfinder_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" 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" help="(-second_nearest_gap) "/>
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127 <param name="param_algorithm_pairfinder_use_identifications" display="radio" type="boolean" truevalue="-algorithm:pairfinder:use_identifications" falsevalue="" checked="false" optional="True" 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)" help="(-use_identifications) "/>
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128 <param name="param_algorithm_pairfinder_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:pairfinder:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
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129 <param name="param_algorithm_pairfinder_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
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130 <param name="param_algorithm_pairfinder_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
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131 <param name="param_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
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132 <option value="Da" selected="true">Da</option>
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133 <option value="ppm">ppm</option>
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134 </param>
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135 <expand macro="advanced_options">
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136 <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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137 <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 (in seconds)" help="(-max_shift) This applies for both directions"/>
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138 <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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139 <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" 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)" help="(-exponent) "/>
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140 <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
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141 <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" 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)" help="(-exponent) "/>
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142 <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
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143 <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
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144 <param name="param_algorithm_pairfinder_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
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145 <param name="param_algorithm_pairfinder_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
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146 <option value="enabled">enabled</option>
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147 <option value="disabled" selected="true">disabled</option>
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148 </param>
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149 </expand>
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150 </inputs>
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151 <outputs>
1
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152 <collection name="out" type="list">
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153 <discover_datasets pattern="__designation_and_ext__" directory="results_out"/>
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154 </collection>
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155
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156 <collection name="trafo_out" type="list">
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157 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/>
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158 </collection>
0
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159 </outputs>
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160 <help>Corrects retention time distortions between maps using a pose clustering approach.
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161
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162
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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163 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help>
70f729e59244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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164 </tool>