annotate MapAlignerPoseClustering.xml @ 10:246847b3a188 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:16:48 +0000
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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@VERSION_SUFFIX@" profile="21.05">
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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 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 mkdir in_cond.in &&
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18 #if $in_cond.in_select == "no"
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19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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21 #else
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22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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23 #end if
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24 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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25 mkdir out &&
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26 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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27 #end if
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28 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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29 mkdir trafo_out &&
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30 mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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31 #end if
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32 #if $reference.file:
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33 mkdir reference.file &&
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34 ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
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35 #end if
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37 ## Main program call
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38
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39 set -o pipefail &&
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40 @EXECUTABLE@ -write_ctd ./ &&
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41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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43 -in
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44 #if $in_cond.in_select == "no"
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45 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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46 #else
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47 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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48 #end if
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49 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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50 -out
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51 ${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), f.ext) for i, f in enumerate($in_cond.in) if f])}
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52 #end if
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53 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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54 -trafo_out
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55 ${' '.join(["'trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])}
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56 #end if
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57 #if $reference.file:
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58 -reference:file
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59 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)'
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60 #end if
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61 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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62 | tee '$stdout'
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63 #end if
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64
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65 ## Postprocessing
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66 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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67 ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])}
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68 #end if
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69 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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70 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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71 #end if]]></command>
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72 <configfiles>
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73 <inputs name="args_json" data_style="paths"/>
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74 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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75 </configfiles>
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76 <inputs>
10
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77 <conditional name="in_cond">
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78 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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79 <option value="no">No: process all datasets jointly</option>
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80 <option value="yes">Yes: process each dataset in an independent job</option>
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81 </param>
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82 <when value="no">
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83 <param 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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84 </when>
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85 <when value="yes">
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86 <param argument="-in" type="data" format="featurexml,mzml" multiple="false" 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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87 </when>
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88 </conditional>
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89 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
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90 <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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91 <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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92 </section>
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93 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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94 <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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95 <section name="superimposer" title="" help="" expanded="false">
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96 <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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97 <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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98 <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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99 <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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100 <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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101 <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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102 <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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103 <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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104 <expand macro="list_string_san" name="dump_buckets"/>
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105 </param>
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106 <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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107 <expand macro="list_string_san" name="dump_pairs"/>
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108 </param>
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109 </section>
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110 <section name="pairfinder" title="" help="" expanded="false">
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111 <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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112 <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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113 <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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114 <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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115 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
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116 <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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117 <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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118 <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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119 </section>
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120 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
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121 <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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122 <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
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123 <option value="Da" selected="true">Da</option>
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124 <option value="ppm">ppm</option>
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125 <expand macro="list_string_san" name="unit"/>
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126 </param>
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127 <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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128 <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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129 </section>
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130 <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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131 <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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132 <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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133 <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" type="select" optional="true" 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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134 <option value="enabled">enabled</option>
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135 <option value="disabled" selected="true">disabled</option>
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136 <expand macro="list_string_san" name="log_transform"/>
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137 </param>
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138 </section>
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139 </section>
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140 </section>
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141 <expand macro="adv_opts_macro">
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142 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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143 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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144 <expand macro="list_string_san" name="test"/>
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145 </param>
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146 </expand>
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147 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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148 <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
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149 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
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150 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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151 </param>
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152 </inputs>
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153 <outputs>
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154 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
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155 <discover_datasets directory="out" recurse="true" pattern="__name_and_ext__"/>
6
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156 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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157 </collection>
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158 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
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159 <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
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160 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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161 </collection>
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162 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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163 <filter>OPTIONAL_OUTPUTS is None</filter>
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164 </data>
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165 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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166 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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167 </data>
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168 </outputs>
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169 <tests><!-- TOPP_MapAlignerPoseClustering_1 -->
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170 <test expect_num_outputs="3">
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171 <section name="adv_opts">
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172 <param name="force" value="false"/>
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173 <param name="test" value="true"/>
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174 </section>
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175 <conditional name="in_cond">
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176 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
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177 </conditional>
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178 <output_collection name="out" count="3"/>
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179 <output_collection name="trafo_out" count="3"/>
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180 <section name="reference">
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181 <param name="index" value="0"/>
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182 </section>
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183 <section name="algorithm">
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184 <param name="max_num_peaks_considered" value="400"/>
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185 <section name="superimposer">
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186 <param name="mz_pair_max_distance" value="0.5"/>
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187 <param name="rt_pair_distance_fraction" value="0.1"/>
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188 <param name="num_used_points" value="2000"/>
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189 <param name="scaling_bucket_size" value="0.005"/>
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190 <param name="shift_bucket_size" value="3.0"/>
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191 <param name="max_shift" value="1000.0"/>
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192 <param name="max_scaling" value="2.0"/>
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193 <param name="dump_buckets" value=""/>
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194 <param name="dump_pairs" value=""/>
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195 </section>
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196 <section name="pairfinder">
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197 <param name="second_nearest_gap" value="2.0"/>
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198 <param name="use_identifications" value="false"/>
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199 <param name="ignore_charge" value="true"/>
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200 <param name="ignore_adduct" value="true"/>
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201 <section name="distance_RT">
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202 <param name="max_difference" value="30.0"/>
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203 <param name="exponent" value="1.0"/>
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204 <param name="weight" value="1.0"/>
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205 </section>
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206 <section name="distance_MZ">
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207 <param name="max_difference" value="0.3"/>
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208 <param name="unit" value="Da"/>
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209 <param name="exponent" value="2.0"/>
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210 <param name="weight" value="1.0"/>
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211 </section>
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212 <section name="distance_intensity">
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213 <param name="exponent" value="1.0"/>
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214 <param name="weight" value="0.0"/>
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215 <param name="log_transform" value="disabled"/>
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216 </section>
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217 </section>
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218 </section>
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219 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
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220 <output name="ctd_out" ftype="xml">
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221 <assert_contents>
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222 <is_valid_xml/>
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223 </assert_contents>
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224 </output>
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225 </test>
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226 <!-- TOPP_MapAlignerPoseClustering_2 -->
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227 <test expect_num_outputs="2">
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228 <section name="adv_opts">
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229 <param name="force" value="false"/>
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230 <param name="test" value="true"/>
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231 </section>
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232 <conditional name="in_cond">
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233 <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/>
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234 </conditional>
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235 <output_collection name="out" count="3"/>
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236 <section name="reference">
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237 <param name="index" value="0"/>
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238 </section>
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239 <section name="algorithm">
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240 <param name="max_num_peaks_considered" value="400"/>
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241 <section name="superimposer">
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242 <param name="mz_pair_max_distance" value="0.5"/>
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243 <param name="rt_pair_distance_fraction" value="0.1"/>
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244 <param name="num_used_points" value="2000"/>
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245 <param name="scaling_bucket_size" value="0.005"/>
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246 <param name="shift_bucket_size" value="3.0"/>
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247 <param name="max_shift" value="1000.0"/>
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248 <param name="max_scaling" value="2.0"/>
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249 <param name="dump_buckets" value=""/>
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250 <param name="dump_pairs" value=""/>
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251 </section>
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252 <section name="pairfinder">
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253 <param name="second_nearest_gap" value="2.0"/>
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254 <param name="use_identifications" value="false"/>
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255 <param name="ignore_charge" value="false"/>
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256 <param name="ignore_adduct" value="true"/>
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257 <section name="distance_RT">
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258 <param name="max_difference" value="100.0"/>
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259 <param name="exponent" value="1.0"/>
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260 <param name="weight" value="1.0"/>
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261 </section>
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262 <section name="distance_MZ">
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263 <param name="max_difference" value="0.3"/>
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264 <param name="unit" value="Da"/>
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265 <param name="exponent" value="2.0"/>
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266 <param name="weight" value="1.0"/>
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267 </section>
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268 <section name="distance_intensity">
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269 <param name="exponent" value="1.0"/>
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270 <param name="weight" value="0.0"/>
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271 <param name="log_transform" value="disabled"/>
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272 </section>
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273 </section>
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274 </section>
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275 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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276 <output name="ctd_out" ftype="xml">
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277 <assert_contents>
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278 <is_valid_xml/>
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279 </assert_contents>
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280 </output>
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281 </test>
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282 <!-- TOPP_MapAlignerPoseClustering_3 -->
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283 <test expect_num_outputs="2">
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284 <section name="adv_opts">
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285 <param name="force" value="false"/>
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286 <param name="test" value="true"/>
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287 </section>
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288 <conditional name="in_cond">
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289 <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
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290 </conditional>
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291 <output_collection name="out" count="2"/>
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292 <section name="reference">
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293 <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/>
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294 <param name="index" value="0"/>
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295 </section>
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296 <section name="algorithm">
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297 <param name="max_num_peaks_considered" value="400"/>
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298 <section name="superimposer">
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299 <param name="mz_pair_max_distance" value="0.5"/>
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300 <param name="rt_pair_distance_fraction" value="0.1"/>
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301 <param name="num_used_points" value="2000"/>
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302 <param name="scaling_bucket_size" value="0.005"/>
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303 <param name="shift_bucket_size" value="3.0"/>
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304 <param name="max_shift" value="1000.0"/>
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305 <param name="max_scaling" value="2.0"/>
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306 <param name="dump_buckets" value=""/>
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307 <param name="dump_pairs" value=""/>
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308 </section>
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309 <section name="pairfinder">
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310 <param name="second_nearest_gap" value="2.0"/>
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311 <param name="use_identifications" value="false"/>
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312 <param name="ignore_charge" value="true"/>
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313 <param name="ignore_adduct" value="true"/>
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314 <section name="distance_RT">
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315 <param name="max_difference" value="30.0"/>
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316 <param name="exponent" value="1.0"/>
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317 <param name="weight" value="1.0"/>
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318 </section>
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319 <section name="distance_MZ">
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320 <param name="max_difference" value="0.3"/>
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321 <param name="unit" value="Da"/>
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322 <param name="exponent" value="2.0"/>
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323 <param name="weight" value="1.0"/>
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324 </section>
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325 <section name="distance_intensity">
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326 <param name="exponent" value="1.0"/>
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327 <param name="weight" value="0.0"/>
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328 <param name="log_transform" value="disabled"/>
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329 </section>
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330 </section>
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331 </section>
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332 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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333 <output name="ctd_out" ftype="xml">
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334 <assert_contents>
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335 <is_valid_xml/>
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336 </assert_contents>
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337 </output>
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338 </test>
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339 <!-- TOPP_MapAlignerPoseClustering_4 -->
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340 <test expect_num_outputs="2">
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341 <section name="adv_opts">
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342 <param name="force" value="false"/>
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343 <param name="test" value="true"/>
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344 </section>
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345 <conditional name="in_cond">
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346 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/>
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347 </conditional>
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348 <output_collection name="trafo_out" count="2"/>
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349 <section name="reference">
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350 <param name="index" value="2"/>
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351 </section>
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352 <section name="algorithm">
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353 <param name="max_num_peaks_considered" value="400"/>
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354 <section name="superimposer">
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355 <param name="mz_pair_max_distance" value="0.5"/>
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356 <param name="rt_pair_distance_fraction" value="0.1"/>
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357 <param name="num_used_points" value="2000"/>
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358 <param name="scaling_bucket_size" value="0.005"/>
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359 <param name="shift_bucket_size" value="3.0"/>
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360 <param name="max_shift" value="1000.0"/>
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361 <param name="max_scaling" value="2.0"/>
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362 <param name="dump_buckets" value=""/>
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363 <param name="dump_pairs" value=""/>
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364 </section>
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365 <section name="pairfinder">
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366 <param name="second_nearest_gap" value="2.0"/>
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367 <param name="use_identifications" value="false"/>
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368 <param name="ignore_charge" value="true"/>
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369 <param name="ignore_adduct" value="true"/>
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370 <section name="distance_RT">
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371 <param name="max_difference" value="30.0"/>
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372 <param name="exponent" value="1.0"/>
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373 <param name="weight" value="1.0"/>
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374 </section>
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375 <section name="distance_MZ">
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376 <param name="max_difference" value="0.3"/>
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377 <param name="unit" value="Da"/>
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378 <param name="exponent" value="2.0"/>
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379 <param name="weight" value="1.0"/>
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380 </section>
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381 <section name="distance_intensity">
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382 <param name="exponent" value="1.0"/>
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383 <param name="weight" value="0.0"/>
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384 <param name="log_transform" value="disabled"/>
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385 </section>
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386 </section>
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387 </section>
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388 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
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389 <output name="ctd_out" ftype="xml">
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390 <assert_contents>
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391 <is_valid_xml/>
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392 </assert_contents>
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393 </output>
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394 </test>
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395 </tests>
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396 <help><![CDATA[Corrects retention time distortions between maps using a pose clustering approach.
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397
0
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398
10
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399 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
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400 <expand macro="references"/>
0
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401 </tool>