Mercurial > repos > galaxyp > openms_assaygeneratormetabo

annotate AssayGeneratorMetabo.xml @ 0:cb9d2162b340 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:46:21 -0400
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children d30e724536fc
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cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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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: [Utilities]-->
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4 <tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Assay library generation from DDA data (Metabolomics)</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">AssayGeneratorMetabo</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 mkdir in_id &&
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22 ${ ' '.join(["ln -s '%s' 'in_id/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _]) }
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23 mkdir out &&
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24
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25 ## Main program call
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26
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 -in
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32 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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33 -in_id
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34 ${' '.join(["'in_id/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _])}
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35 -out
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36 'out/output.${out_type}'
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37
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38 ## Postprocessing
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39 && mv 'out/output.${out_type}' '$out'
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40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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42 #end if]]></command>
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43 <configfiles>
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44 <inputs name="args_json" data_style="paths"/>
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45 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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46 </configfiles>
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47 <inputs>
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48 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
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49 <param name="in_id" argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
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50 <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)">
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51 <option value="tsv">tabular (tsv)</option>
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52 <option value="traML">traml</option>
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53 <option value="pqp">pqp</option>
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54 </param>
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55 <param name="fragment_annotation" argument="-fragment_annotation" display="radio" type="select" optional="false" label="Fragment annotation method" help="">
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56 <option value="none" selected="true">none</option>
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57 <option value="sirius">sirius</option>
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58 <expand macro="list_string_san"/>
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59 </param>
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60 <param name="method" argument="-method" display="radio" type="select" optional="false" label="Spectrum with the highest precursor intensity or a consensus spectrum ist used for assay library construction (if no fragment annotation is used)" help="">
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61 <option value="highest_intensity" selected="true">highest_intensity</option>
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62 <option value="consensus_spectrum">consensus_spectrum</option>
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63 <expand macro="list_string_san"/>
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64 </param>
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65 <param name="use_exact_mass" argument="-use_exact_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use exact mass for fragment annotation" help=""/>
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66 <param name="exclude_ms2_precursor" argument="-exclude_ms2_precursor" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Excludes precursor in ms2 from transition list" help=""/>
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67 <param name="precursor_mz_distance" argument="-precursor_mz_distance" type="float" optional="true" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
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68 <param name="precursor_rt_tolerance" argument="-precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
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69 <param name="use_known_unknowns" argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/>
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70 <param name="min_transitions" argument="-min_transitions" type="integer" optional="true" value="3" label="Minimal number of transitions" help=""/>
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71 <param name="max_transitions" argument="-max_transitions" type="integer" optional="true" value="3" label="Maximal number of transitions" help=""/>
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72 <param name="cosine_similarity_threshold" argument="-cosine_similarity_threshold" type="float" optional="true" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/>
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73 <param name="transition_threshold" argument="-transition_threshold" type="float" optional="true" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/>
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74 <param name="out_workspace_directory" argument="-out_workspace_directory" type="text" optional="true" value="" label="Output directory for SIRIUS workspace" help="">
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75 <expand macro="list_string_san"/>
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76 </param>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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77 <section name="deisotoping" title="deisotoping" help="" expanded="false">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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78 <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" optional="true" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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80 <param name="fragment_unit" argument="-deisotoping:fragment_unit" display="radio" type="select" optional="false" label="Unit of the fragment tolerance" help="">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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81 <option value="ppm" selected="true">ppm</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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82 <option value="Da">Da</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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83 <expand macro="list_string_san"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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84 </param>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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85 <param name="min_charge" argument="-deisotoping:min_charge" type="integer" optional="true" min="1" value="1" label="The minimum charge considered" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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86 <param name="max_charge" argument="-deisotoping:max_charge" type="integer" optional="true" min="1" value="1" label="The maximum charge considered" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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87 <param name="min_isopeaks" argument="-deisotoping:min_isopeaks" type="integer" optional="true" min="2" value="2" label="The minimum number of isotopic peaks (at least 2) required for an isotopic cluste" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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88 <param name="max_isopeaks" argument="-deisotoping:max_isopeaks" type="integer" optional="true" min="3" value="3" label="The maximum number of isotopic peaks (at least 2) considered for an isotopic cluste" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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89 <param name="keep_only_deisotoped" argument="-deisotoping:keep_only_deisotoped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only monoisotopic peaks of fragments with isotopic pattern are retained" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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90 <param name="annotate_charge" argument="-deisotoping:annotate_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Annotate the charge to the peaks" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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91 </section>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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92 <section name="preprocessing" title="Preprocessing" help="" expanded="false">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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93 <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Features have to have at least x MassTraces" help="To use this parameter feature_only is neccessary"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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94 <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="0.005" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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95 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help="">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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96 <option value="Da" selected="true">Da</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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97 <option value="ppm">ppm</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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98 <expand macro="list_string_san"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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99 </param>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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100 <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="integer" optional="true" value="5" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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101 <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" optional="true" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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102 <param name="feature_only" argument="-preprocessing:feature_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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103 <param name="no_masstrace_info_isotope_pattern" argument="-preprocessing:no_masstrace_info_isotope_pattern" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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104 </section>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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105 <section name="sirius" title="Parameters for SIRIUS and CSI:FingerID" help="" expanded="false">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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106 <param name="profile" argument="-sirius:profile" display="radio" type="select" optional="false" label="Specify the used analysis profile" help="">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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107 <option value="qtof" selected="true">qtof</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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108 <option value="orbitrap">orbitrap</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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109 <option value="fticr">fticr</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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110 <expand macro="list_string_san"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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111 </param>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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112 <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of candidates in the SIRIUS output" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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113 <param name="database" argument="-sirius:database" type="select" optional="false" label="search formulas in given database" help="">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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114 <option value="all" selected="true">all</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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115 <option value="chebi">chebi</option>
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116 <option value="custom">custom</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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117 <option value="kegg">kegg</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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118 <option value="bio">bio</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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119 <option value="natural products">natural products</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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120 <option value="pubmed">pubmed</option>
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121 <option value="hmdb">hmdb</option>
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122 <option value="biocyc">biocyc</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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123 <option value="hsdb">hsdb</option>
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124 <option value="knapsack">knapsack</option>
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125 <option value="biological">biological</option>
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126 <option value="zinc bio">zinc bio</option>
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127 <option value="gnps">gnps</option>
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128 <option value="pubchem">pubchem</option>
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129 <option value="mesh">mesh</option>
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130 <option value="maconda">maconda</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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131 <expand macro="list_string_san"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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132 </param>
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133 <param name="noise" argument="-sirius:noise" type="integer" optional="true" min="0" value="0" label="median intensity of noise peaks" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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134 <param name="ppm_max" argument="-sirius:ppm_max" type="integer" optional="true" value="10" label="allowed ppm for decomposing masses" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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135 <param name="isotope" argument="-sirius:isotope" display="radio" type="select" optional="false" label="how to handle isotope pattern data" help="Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring. Use 'omit' to ignore isotope pattern">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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136 <option value="score">score</option>
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137 <option value="filter">filter</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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138 <option value="both" selected="true">both</option>
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139 <option value="omit">omit</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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140 <expand macro="list_string_san"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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141 </param>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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142 <param name="elements" argument="-sirius:elements" type="text" optional="true" value="CHNOP[5]S[8]Cl[1]" label="The allowed elements" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1]">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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143 <expand macro="list_string_san"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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144 </param>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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145 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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146 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/>
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147 <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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148 <param name="cores" argument="-sirius:cores" type="integer" optional="true" min="1" value="1" label="The number of cores SIRIUS is allowed to use on the system" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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149 <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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150 <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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151 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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152 <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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153 </section>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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154 <expand macro="adv_opts_macro">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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155 <param name="precursor_recalibration_window" argument="-precursor_recalibration_window" type="float" optional="true" value="0.1" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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156 <param name="precursor_recalibration_window_unit" argument="-precursor_recalibration_window_unit" display="radio" type="select" optional="false" label="Unit of the precursor_mz_tolerance_annotation" help="">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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157 <option value="Da" selected="true">Da</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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158 <option value="ppm">ppm</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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159 <expand macro="list_string_san"/>
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160 </param>
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161 <param name="min_fragment_mz" argument="-min_fragment_mz" type="float" optional="true" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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162 <param name="max_fragment_mz" argument="-max_fragment_mz" type="float" optional="true" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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163 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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164 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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165 <expand macro="list_string_san"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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166 </param>
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167 </expand>
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168 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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169 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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170 </param>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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171 </inputs>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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172 <outputs>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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173 <data name="out" label="${tool.name} on ${on_string}: out">
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174 <change_format>
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175 <when input="out_type" value="pqp" format="pqp"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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176 <when input="out_type" value="traML" format="traml"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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177 <when input="out_type" value="tsv" format="tabular"/>
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178 </change_format>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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179 </data>
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180 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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181 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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182 </data>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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183 </outputs>
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184 <tests>
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185 <expand macro="autotest_AssayGeneratorMetabo"/>
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186 <expand macro="manutest_AssayGeneratorMetabo"/>
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187 </tests>
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188 <help><![CDATA[Assay library generation from DDA data (Metabolomics)
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189
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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190
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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191 For more information, visit http://www.openms.de/documentation/UTILS_AssayGeneratorMetabo.html]]></help>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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192 <expand macro="references"/>
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193 </tool>