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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
author computational-metabolomics
date Tue, 14 Jul 2020 07:42:34 -0400
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3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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1 <tool id="metfrag_vis" name="MetFrag Vis" version="2.4.5+galaxy0" profile="18.01">
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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2 <description>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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3 Visualisation for MetFrag results
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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4 </description>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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5 <requirements>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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6 <requirement type="package" version="2.4.5">metfrag</requirement>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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7 <requirement type="package" version="0.9">cdk-inchi-to-svg</requirement>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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8 <requirement type="package" version="3.7.3">python</requirement>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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9 <requirement type="package" version="1.0.4">pubchempy</requirement>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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10 <requirement type="package">matplotlib</requirement>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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11 <requirement type="package">requests</requirement>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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12 <requirement type="package">numpy</requirement>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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13 </requirements>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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14 <stdio>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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15 <regex match="Cannot allocate memory"
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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16 source="stderr"
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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17 level="fatal_oom"
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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18 description="Out of memory error occurred" />
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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19 </stdio>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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20 <command detect_errors="exit_code">
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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21 <![CDATA[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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22 python '$__tool_directory__/metfrag-vis.py'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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23 -i $metfrag_vis_input
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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24 -o $metfrag_vis_output
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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25 -m $metfrag_vis_hits_limit
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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26 $metfrag_synonyms
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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27 $metfrag_classyfire
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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28 ]]></command>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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29 <inputs>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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30 <param argument="-i" name="metfrag_vis_input" type="data" format="tsv,tabular" multiple="False" optional="False" label="MetFrag result file (Output tabular file from MetFrag tool)" />
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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31 <param argument="-m" name="metfrag_vis_hits_limit" type="text" value="10" label="MetFrag Hits Limit" optional="False" help="Limit of candidate hits returned per compound" />
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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32 <param argument="-s" name="metfrag_synonyms" type="boolean" truevalue="-s" falsevalue="" checked="true" label="Synonyms" help="Fetch synonyms for each candidate from PubChem"/>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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33 <param argument="-c" name="metfrag_classyfire" type="boolean" truevalue="-c" falsevalue="" label="ClassyFire" help="Fetch compound classes for each candidate using ClassyFire"/>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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34 </inputs>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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35 <outputs>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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36 <data name="metfrag_vis_output" format="html" label="Summary HTML file" />
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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37 </outputs>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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38
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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39 <tests>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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40 <test>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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41 <param name="metfrag_vis_input" value="metfrag_vis_input.tabular"/>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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42 <output name="metfrag_vis_output" file="metfrag_vis_output.html" compare="sim_size"/>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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43 </test>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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44 </tests>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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45
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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46 <help>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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47 ---------------------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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48 MetFrag Visualisation
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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49 ---------------------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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50
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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51 Description
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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52 -----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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53
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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54 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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55 a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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56 are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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57 matches gives hints to the quality of the candidate spectrum assignment.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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58
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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59 This module summarises the results generated by MetFrag. It takes the (sometimes very large) output tabular file, parses the file and enriches it with images of the spectra showing the extracted and matched peaks and putative structures of the compound candidates. The module supports limiting the results per compound (default 10 candidates). Results can be enriched with further information from PubChem and ClassyFire to make it easier to select candidates. The information is summarised in a HTML5 file which can be viewed directly in Galaxy.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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60
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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61 Website: http://ipb-halle.github.io/MetFrag/
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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62
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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63 Parameters
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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64 ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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65
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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66 **\1. Tabular file**
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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67
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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68 Tabular file created using the *MetFrag* tool.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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69
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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70 **\2. MetFrag Hits Limit**
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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71
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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72 Defines the limit of candidates returned per compound.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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73
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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74 **\3. Synonyms**
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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75
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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76 If set to True, synonyms for each candidate are fetched from PubChem.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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77
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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78 **\4. ClassyFire**
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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79
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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80 If set to True, compound classes are fetched for each candidate using ClassyFire.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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81
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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82 Output
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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83 -------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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84
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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85 The output is similar to the MetFrag results tabular, but enriched with additional images of spectra, compound candidates and (if enabled) compound classes, alternative names and links to online services.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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86
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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87 +-------------+--------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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88 | adduct | name |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
diff changeset
89 +-------------+--------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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90 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
diff changeset
91 +-------------+--------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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92 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
diff changeset
93 +-------------+--------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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94 | ... | ... |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
95 +-------------+--------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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96
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
97 Table continued (these columns are derived from the MetFrag result):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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98
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
99 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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100 |...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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101 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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102 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
103 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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104 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
diff changeset
105 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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106 |...| ... | ... | ... | ... |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
107 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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108
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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109
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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110 Table continued (columns are derived from the MetFrag result):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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111
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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112 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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113 |...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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114 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
115 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | 6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 206 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
diff changeset
116 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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117 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | (3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 5793 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
diff changeset
118 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
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119 |...| ... | ... | ... | ... | ... |...|
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
120 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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121
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
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122 Table continued (columns are derived from the MetFrag result):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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123
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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124
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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125 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
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126 |...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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127 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
diff changeset
128 |...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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129 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
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130 |...| 4 | 5 | 2.84566828424078 | C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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131 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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132 |...| ... | ... | ... | ... | ... | ... | ... |
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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133 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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134
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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135 Additional notes
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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136 --------------------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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137
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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138 This module queries the online services PubChem and ClassyFire.
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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139
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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140 Feunang YD, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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141 Greiner R, Wishart DS (2016): ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J Cheminform 8:61. doi: 10.1186/s13321-016-0174-y
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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142
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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143 Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2019): PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 8;47(D1):D1102-D1109. doi: 10.1093/nar/gky1033
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
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144
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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diff changeset
145 Developers and contributors
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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146 ---------------------------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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147 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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148 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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149 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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150 </help>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
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151 <citations>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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152 <citation type="doi">10.1186/s13321-016-0115-9</citation>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
parents:
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153 </citations>
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
computational-metabolomics
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154 </tool>