Mercurial > repos > galaxyp > openms_featurefindermetaboident

annotate FeatureFinderMetaboIdent.xml @ 5:a93b05cf3a38 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:30:15 +0000
parents ae20e8a6d309
children
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539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 <!--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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a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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2 <!--Proposed Tool Section: [Quantitation]-->
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ae20e8a6d309 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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3 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Detects features in MS1 data based on metabolite identifications</description>
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539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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5 <macros>
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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6 <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</token>
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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7 <import>macros.xml</import>
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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8 </macros>
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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9 <expand macro="requirements"/>
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 <expand macro="stdio"/>
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 @EXT_FOO@
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 #import re
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 ## Preprocessing
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 mkdir in &&
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a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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18 mkdir id &&
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a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 mkdir out &&
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 mkdir lib_out &&
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 #end if
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 mkdir chrom_out &&
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 #end if
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a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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27 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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28 mkdir trafo_out &&
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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29 #end if
0
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 mkdir candidates_out &&
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 #end if
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 ## Main program call
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 set -o pipefail &&
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 @EXECUTABLE@ -write_ctd ./ &&
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38 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 -in
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 -id
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 -out
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 'out/output.${gxy2omsext("featurexml")}'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 -lib_out
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 'lib_out/output.${gxy2omsext("traml")}'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 #end if
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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50 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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51 -chrom_out
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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52 'chrom_out/output.${gxy2omsext("mzml")}'
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53 #end if
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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54 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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55 -trafo_out
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 'trafo_out/output.${gxy2omsext("trafoxml")}'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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57 #end if
5
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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58 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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59 -candidates_out
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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60 'candidates_out/output.${gxy2omsext("txt")}'
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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61 #end if
0
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62 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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63 | tee '$stdout'
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64 #end if
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 ## Postprocessing
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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67 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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68 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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69 && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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70 #end if
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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71 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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72 && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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73 #end if
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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74 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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75 && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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76 #end if
5
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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77 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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78 && mv 'candidates_out/output.${gxy2omsext("txt")}' '$candidates_out'
a93b05cf3a38 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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79 #end if
0
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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80 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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81 && mv '@EXECUTABLE@.ctd' '$ctd_out'
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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82 #end if]]></command>
539b683e9752 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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83 <configfiles>
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84 <inputs name="args_json" data_style="paths"/>
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85 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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86 </configfiles>
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87 <inputs>
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88 <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
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89 <param argument="-id" type="data" format="tabular" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
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90 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
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91 <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
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92 <param name="rt_window" argument="-extract:rt_window" type="float" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
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93 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
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94 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
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95 </section>
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96 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
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97 <param name="peak_width" argument="-detect:peak_width" type="float" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
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98 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
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99 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
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100 </section>
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101 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
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102 <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help="">
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103 <option value="symmetric" selected="true">symmetric</option>
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104 <option value="asymmetric">asymmetric</option>
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105 <option value="none">none</option>
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106 <expand macro="list_string_san" name="type"/>
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107 </param>
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108 <param name="add_zeros" argument="-model:add_zeros" type="float" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
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109 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
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110 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
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111 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
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112 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
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113 <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
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114 <param name="boundaries" argument="-model:check:boundaries" type="float" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
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115 <param name="width" argument="-model:check:width" type="float" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
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116 <param name="asymmetry" argument="-model:check:asymmetry" type="float" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
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117 </section>
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118 </section>
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119 <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
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120 <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
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121 <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
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122 </section>
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123 <expand macro="adv_opts_macro">
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124 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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125 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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126 <expand macro="list_string_san" name="test"/>
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127 </param>
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128 </expand>
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129 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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130 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
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131 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
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132 <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option>
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133 <option value="candidates_out_FLAG">candidates_out (Optional output file: Feature candidates (before filtering and model fitting))</option>
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134 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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135 </param>
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136 </inputs>
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137 <outputs>
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138 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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139 <data name="lib_out" label="${tool.name} on ${on_string}: lib_out" format="traml">
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140 <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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141 </data>
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142 <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
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143 <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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144 </data>
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145 <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
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146 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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147 </data>
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148 <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="txt">
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149 <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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150 </data>
0
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151 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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152 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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153 </data>
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154 </outputs>
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155 <tests>
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156 <!-- TOPP_FeatureFinderMetaboIdent_1 -->
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157 <test expect_num_outputs="2">
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158 <section name="adv_opts">
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159 <param name="force" value="false"/>
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160 <param name="test" value="true"/>
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161 </section>
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162 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
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163 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
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164 <output name="out" value="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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165 <section name="extract">
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166 <param name="mz_window" value="5.0"/>
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167 <param name="rt_window" value="20.0"/>
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168 <param name="n_isotopes" value="2"/>
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169 <param name="isotope_pmin" value="0.0"/>
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170 </section>
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171 <section name="detect">
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172 <param name="peak_width" value="3.0"/>
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173 <param name="min_peak_width" value="0.2"/>
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174 <param name="signal_to_noise" value="0.8"/>
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175 </section>
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176 <section name="model">
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177 <param name="type" value="symmetric"/>
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178 <param name="add_zeros" value="0.2"/>
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179 <param name="unweighted_fit" value="false"/>
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180 <param name="no_imputation" value="false"/>
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181 <param name="each_trace" value="false"/>
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182 <section name="check">
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183 <param name="min_area" value="1.0"/>
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184 <param name="boundaries" value="0.5"/>
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185 <param name="width" value="10.0"/>
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186 <param name="asymmetry" value="10.0"/>
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187 </section>
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188 </section>
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189 <section name="EMGScoring">
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190 <param name="max_iteration" value="100"/>
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191 <param name="init_mom" value="false"/>
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192 </section>
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193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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194 <output name="ctd_out" ftype="xml">
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195 <assert_contents>
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196 <is_valid_xml/>
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197 </assert_contents>
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198 </output>
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199 <assert_stdout>
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200 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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201 </assert_stdout>
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202 </test>
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203 </tests>
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204 <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
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205
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206
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207 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMetaboIdent.html]]></help>
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208 <expand macro="references"/>
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209 </tool>