Mercurial > repos > galaxyp > openms_mapalignerposeclustering

annotate MapAlignerPoseClustering.xml @ 8:d17db97d139f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:35:17 +0000
parents e237cb433a92
children 246847b3a188
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304c13ce9577 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Map Alignment]-->
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4 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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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 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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22 mkdir out &&
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23 #end if
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24 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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25 mkdir trafo_out &&
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26 #end if
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27 #if $reference.file:
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28 mkdir reference.file &&
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29 ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
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30 #end if
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32 ## Main program call
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34 set -o pipefail &&
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35 @EXECUTABLE@ -write_ctd ./ &&
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36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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38 -in
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39 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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40 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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41 -out
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42 ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
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43 #end if
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44 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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45 -trafo_out
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46 ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
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47 #end if
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48 #if $reference.file:
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49 -reference:file
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50 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)'
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51 #end if
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52 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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53 | tee '$stdout'
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54 #end if
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55
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56 ## Postprocessing
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57 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
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59 #end if
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60 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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61 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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62 #end if]]></command>
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63 <configfiles>
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64 <inputs name="args_json" data_style="paths"/>
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65 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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66 </configfiles>
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67 <inputs>
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68 <param name="in" argument="-in" type="data" format="featurexml,mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
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69 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
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70 <param name="file" argument="-reference:file" type="data" format="featurexml,mzml" optional="true" label="File to use as reference (same file format as input files required)" help=" select featurexml,mzml data sets(s)"/>
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71 <param name="index" argument="-reference:index" type="integer" optional="true" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
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72 </section>
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73 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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74 <param name="max_num_peaks_considered" argument="-algorithm:max_num_peaks_considered" type="integer" optional="true" min="-1" value="1000" label="The maximal number of peaks/features to be considered per map" help="To use all, set to '-1'"/>
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75 <section name="superimposer" title="" help="" expanded="false">
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76 <param name="mz_pair_max_distance" argument="-algorithm:superimposer:mz_pair_max_distance" type="float" optional="true" min="0.0" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="This condition applies to the pairs considered in hashing"/>
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77 <param name="rt_pair_distance_fraction" argument="-algorithm:superimposer:rt_pair_distance_fraction" type="float" optional="true" min="0.0" max="1.0" 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" help="(i.e., max - min). "/>
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78 <param name="num_used_points" argument="-algorithm:superimposer:num_used_points" type="integer" optional="true" min="-1" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="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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79 <param name="scaling_bucket_size" argument="-algorithm:superimposer:scaling_bucket_size" type="float" optional="true" min="0.0" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
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80 <param name="shift_bucket_size" argument="-algorithm:superimposer:shift_bucket_size" type="float" optional="true" min="0.0" 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="A good choice for this would be about the time between consecutive MS scans"/>
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81 <param name="max_shift" argument="-algorithm:superimposer:max_shift" type="float" optional="true" min="0.0" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="This applies for both directions"/>
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82 <param name="max_scaling" argument="-algorithm:superimposer:max_scaling" type="float" optional="true" min="1.0" value="2.0" label="Maximal scaling which is considered during histogramming" help="The minimal scaling is the reciprocal of this"/>
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83 <param name="dump_buckets" argument="-algorithm:superimposer:dump_buckets" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="A serial number for each invocation will be appended automatically">
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84 <expand macro="list_string_san"/>
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85 </param>
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86 <param name="dump_pairs" argument="-algorithm:superimposer:dump_pairs" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="A serial number for each invocation will be appended automatically">
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87 <expand macro="list_string_san"/>
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88 </param>
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89 </section>
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90 <section name="pairfinder" title="" help="" expanded="false">
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91 <param name="second_nearest_gap" argument="-algorithm:pairfinder:second_nearest_gap" type="float" optional="true" min="1.0" 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=""/>
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92 <param name="use_identifications" argument="-algorithm:pairfinder:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" 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=""/>
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93 <param name="ignore_charge" argument="-algorithm:pairfinder:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
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94 <param name="ignore_adduct" argument="-algorithm:pairfinder:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
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95 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
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96 <param name="max_difference" argument="-algorithm:pairfinder:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
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97 <param name="exponent" argument="-algorithm:pairfinder:distance_RT:exponent" type="float" optional="true" min="0.0" 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=""/>
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98 <param name="weight" argument="-algorithm:pairfinder:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
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99 </section>
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100 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
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101 <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
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102 <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
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103 <option value="Da" selected="true">Da</option>
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104 <option value="ppm">ppm</option>
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105 <expand macro="list_string_san"/>
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106 </param>
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107 <param name="exponent" argument="-algorithm:pairfinder:distance_MZ:exponent" type="float" optional="true" min="0.0" 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=""/>
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108 <param name="weight" argument="-algorithm:pairfinder:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
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109 </section>
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110 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
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111 <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" optional="true" min="0.0" 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=""/>
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112 <param name="weight" argument="-algorithm:pairfinder:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
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113 <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="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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114 <option value="enabled">enabled</option>
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115 <option value="disabled" selected="true">disabled</option>
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116 <expand macro="list_string_san"/>
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117 </param>
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118 </section>
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119 </section>
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120 </section>
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121 <expand macro="adv_opts_macro">
8
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122 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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123 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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124 <expand macro="list_string_san"/>
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125 </param>
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126 </expand>
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127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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128 <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
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129 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
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130 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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131 </param>
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132 </inputs>
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133 <outputs>
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134 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
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135 <discover_datasets directory="out" pattern="__name_and_ext__"/>
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136 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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137 </collection>
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138 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
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139 <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
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140 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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141 </collection>
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142 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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143 <filter>OPTIONAL_OUTPUTS is None</filter>
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144 </data>
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145 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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146 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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147 </data>
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148 </outputs>
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149 <tests>
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150 <expand macro="autotest_MapAlignerPoseClustering"/>
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151 <expand macro="manutest_MapAlignerPoseClustering"/>
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152 </tests>
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153 <help><![CDATA[Corrects retention time distortions between maps using a pose clustering approach.
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156 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
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157 <expand macro="references"/>
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158 </tool>