Mercurial > repos > recetox > matchms_remove_key
annotate help.xml @ 11:fbdb2ae524df draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 129488bfd91735fc55fe32edb1079c24eee7b2d3
author | recetox |
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date | Thu, 14 Nov 2024 15:13:34 +0000 |
parents | 8c98b3cb320e |
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ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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1 <macros> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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2 <token name="@HELP_matchms@"> |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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3 Documentation |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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4 The Python library matchms provides functions to convert, filter and compare mass spectrometry data. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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5 For an overview of the different galaxy modules, see the figure below. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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6 For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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7 and https://matchms.readthedocs.io/en/latest/ for the Python API. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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8 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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9 Overview |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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10 .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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11 :width: 3120 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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12 :height: 1686 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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13 :scale: 30 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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14 :alt: Overview of different matchms galaxytools and how they are connected. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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15 </token> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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16 <token name="@HELP_matchms_networking@"> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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17 <![CDATA[ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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18 Documentation |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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19 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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20 and https://matchms.readthedocs.io/en/latest/. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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21 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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22 **Upstream Tools** |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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23 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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24 matchms similarity |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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25 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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26 **Downstream Tools** |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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27 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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28 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape). |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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29 ]]> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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30 </token> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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31 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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32 <token name="@HELP_formatter@"> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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33 <![CDATA[ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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34 Usage |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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35 This tool creates user friendly tables from the similarity scores produced by **matchms similarity**. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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36 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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37 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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38 Input Table Format |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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39 The tool expects a JSON file containing serialized matchms Scores object. |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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40 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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41 Output Table Format |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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42 +----------+-----------+---------+--------+ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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43 | query | reference | matches | scores | |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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44 +==========+===========+=========+========+ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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45 | C001 | Glycine | 6 | 0.5 | |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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46 +----------+-----------+---------+--------+ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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47 | C002 | Glycine | 3 | 0.34 | |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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48 +----------+-----------+---------+--------+ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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49 | ... | ... | ... | ... | |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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50 +----------+-----------+---------+--------+ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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51 ]]> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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52 </token> |
8
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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53 </macros> |