Mercurial > repos > computational-metabolomics > cfmid
annotate cfmid.xml @ 0:41c4de0ed4ec draft default tip
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
author | computational-metabolomics |
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date | Wed, 15 Nov 2023 16:28:04 +0000 |
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41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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1 <tool id="cfmid" name="CFM-ID" version="33"> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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2 <description></description> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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3 <requirements> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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4 <requirement type="package" version="33">cfm</requirement> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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5 </requirements> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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6 <command detect_errors="exit_code"> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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7 <![CDATA[ |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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8 #set $tool_directory = $getVar('__tool_directory__', '../../../../tools/cfm') |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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9 python $tool_directory/cfmid.py |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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10 --input "$input" |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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11 --db_local '$db_local' |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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12 --ppm_db $ppm_db |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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13 --num_highest $num_highest |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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14 --ppm_mass_tol $ppm_mass_tol |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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15 --abs_mass_tol $abs_mass_tol |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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16 --polarity $polarity |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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17 --score_type $score_type |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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18 --results '$results' |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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19 --tool_directory '$tool_directory' |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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20 ]]></command> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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21 <inputs> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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22 <param argument="--input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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23 <param argument="--db_local" type="data" format="tsv,tabular" label="Local Database (CSV)"/> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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24 <param argument="--ppm_db" type="float" value="5.0" label="Mass tolerance in ppm to use when matching candidates in the database"/> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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25 <param argument="--num_highest" type="integer" value="10" label="The number of (ranked) candidates to return"/> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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26 <param argument="--ppm_mass_tol" type="float" value="10.0" label="Mass tolerance in ppm to use when matching peaks within the dot product comparison"/> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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27 <param argument="--abs_mass_tol" type="float" value="0.01" label="Mass tolerance in abs Da to use when matching peaks within the dot product comparison (will use higher resulting tolerance of ppm and abs)"/> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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28 <param argument="--polarity" type="select" label="Ion Mode"> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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29 <option value="pos" selected="true">Positive</option> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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30 <option value="neg">Negative</option> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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31 </param> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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32 <param argument="--score_type" type="select" label="The type of scoring function to use when comparing spectra"> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
computational-metabolomics
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33 <option value="Jaccard" selected="true">Jaccard index</option> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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34 <option value="DotProduct">Dot Product</option> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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35 </param> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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36 <param argument="--prob_thresh" type="float" value="0.001" label="The probability below which to prune unlikely fragmentations"/> |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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37 </inputs> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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38 <outputs> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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39 <data name="results" format="tsv" label="${tool.name} on ${on_string}: Annotations" /> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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40 </outputs> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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41 <tests> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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42 <test> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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43 <param name="input" value="input.msp"/> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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44 <param name="db_local" value="db.tsv"/> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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45 <param name="ppm_db" value="10.0"/> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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46 <output name="results" file="annotations.tsv"/> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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47 </test> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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48 </tests> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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49 <help> |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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50 ------ |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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51 CFM-ID |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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52 ------ |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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53 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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54 Description |
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55 ----------- |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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56 |
41c4de0ed4ec
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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57 Galaxy wrapper for CFM-ID tool. CFM-ID provides a method for accurately and efficiently identifying metabolites in spectra generated by electrospray tandem mass spectrometry (ESI-MS/MS). The program uses Competitive Fragmentation Modeling to produce a probabilistic generative model for the MS/MS fragmentation process and machine learning techniques to adapt the model parameters from data. |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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58 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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59 Website: https://web.archive.org/web/20230827220748/https://cfmid.wishartlab.com/ |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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60 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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61 Parameters |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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62 ---------- |
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63 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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64 **\1. MSP file** |
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65 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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66 MSP file |
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67 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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68 **\2. Database containing InChI (or SMILES)** |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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69 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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70 The database is used to fetch the candidates for the precursor. The candidates are "in silico" fragmented by CFMID and then the spectras are matched against those in the MSP. |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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71 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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72 Custom database file in **tsv** or "tabular" format with the following structure: |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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73 |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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74 +-------------+------------------+----------+---------------------------------------------+----------------------+ |
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75 | Identifier | MonoisotopicMass | SMILES | InChI | Name | |
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76 +-------------+------------------+----------+---------------------------------------------+----------------------+ |
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77 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine | |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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78 +-------------+------------------+----------+---------------------------------------------+----------------------+ |
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79 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide | |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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80 +-------------+------------------+----------+---------------------------------------------+----------------------+ |
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81 | ... | ... | ... | ... | ... | |
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82 +-------------+------------------+----------+---------------------------------------------+----------------------+ |
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83 |
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84 **\3. Mass tolerance in ppm to use when matching candidates to the database** |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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85 |
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86 **\4. Mass tolerance in ppm to use when matching peaks within the Dot Product comparison** |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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87 |
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88 **\5. The number of (ranked) candidates to return** |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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89 |
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90 Set the top X candidates to return or use "-1" to return all of them, including those that the score is 0. |
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91 |
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92 **\6. Ion Mode** |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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93 |
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94 * Positive: For [M+H]+ adduct. |
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95 |
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96 * Negative: For [M-H]- adduct. |
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97 |
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98 **\7. The type of scoring function to use when comparing spectra** |
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planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
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99 |
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100 * Jaccard: The Jaccard coefficient measures similarity between finite sample sets, and is defined as the size of the intersection divided by the size of the union of the sample sets. |
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101 |
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102 * Dot Product: The product of the Euclidean magnitudes of the two vectors and the cosine of the angle between them. |
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103 |
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104 |
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105 Developers and contributors |
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106 --------------------------- |
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107 |
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108 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)** |
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109 - **Matthias Bernt** (m.bernt@ufz.de) - Helmholtz Centre for Environmental Research - UFZ |
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110 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)** |
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111 </help> |
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112 <citations> |
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113 <citation type="doi">10.1093/nar/gku436</citation> |
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114 </citations> |
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115 </tool> |