Mercurial > repos > recetox > matchms_split
annotate matchms_split.xml @ 2:86de39226109 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 701733d99742a8e567ed6db7384be66c5ecb4a58
author | recetox |
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date | Thu, 18 May 2023 13:24:40 +0000 |
parents | 169c72b2ce79 |
children | 0cf68b536cd1 |
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169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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1 <tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy0" python_template_version="3.7"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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2 <macros> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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3 <import>macros.xml</import> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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4 </macros> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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5 |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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6 <expand macro="creator"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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7 |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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8 <requirements> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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9 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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10 </requirements> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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11 |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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12 <command detect_errors='exit_code'><![CDATA[ |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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13 python3 '$__tool_directory__/matchms_split.py' |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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14 --filename '$msp_input' |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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15 --method '${method.split_type}' |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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16 --outdir 'output' |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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17 #if $method.split_type == "chunk-size" |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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18 --parameter ${method.chunk_size} |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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19 #else if $method.split_type == "num-chunks" |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
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20 --parameter ${method.num_chunks} |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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21 #end if |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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22 ]]></command> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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23 <inputs> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
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24 <param type="data" name="msp_input" format="msp" |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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25 help="Spectral library (.msp) to split into smaller chunks. Requires keyword 'compound_name', 'compoundname' or 'name' to identify individual spectra using the one-per-file method."/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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26 <conditional name="method"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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27 <param name="split_type" type="select" label="Splitting method" display="radio" help="Method on how to split the library."> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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28 <option value="chunk-size" selected="true">Split into chunks of specified size</option> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
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29 <option value="num-chunks">Split into specified number of chunks</option> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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30 <option value="one-per-file">Split to one spectrum per file</option> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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31 </param> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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32 <when value="chunk-size"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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33 <param name="chunk_size" type="integer" value="1000" min="2" help="Number of spectra per output chunks."/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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34 </when> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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35 <when value="num-chunks"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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36 <param name="num_chunks" type="integer" value="5" min="2" help="Number of chunks into which to split the library."/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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37 </when> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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38 <when value="one-per-file" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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39 </conditional> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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40 </inputs> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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41 <outputs> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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42 <collection format="msp" name="sample" type="list"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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43 <discover_datasets pattern="__designation_and_ext__" ext="msp" directory="output"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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44 </collection > |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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45 </outputs> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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46 <tests> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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47 <test> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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48 <param name="msp_input" value="split/sample_input.msp" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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49 <param name="split_type" value="one-per-file" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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50 <output_collection name="sample" type="list"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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51 <element name="1NITROPYRENE" file="split/one-per-file/1NITROPYRENE.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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52 <element name="35DICHLOROPHENOL" file="split/one-per-file/35DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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53 <element name="34DICHLOROPHENOL" file="split/one-per-file/34DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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54 <element name="26DICHLOROPHENOL" file="split/one-per-file/26DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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55 <element name="25DICHLOROPHENOL" file="split/one-per-file/25DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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56 <element name="24DINITROPHENOL" file="split/one-per-file/24DINITROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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57 <element name="24DICHLOROPHENOL" file="split/one-per-file/24DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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58 <element name="246TRICHLOROPHENOL" file="split/one-per-file/246TRICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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59 <element name="245TRICHLOROPHENOL" file="split/one-per-file/245TRICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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60 <element name="23DICHLOROPHENOL" file="split/one-per-file/23DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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61 </output_collection> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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62 </test> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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63 <test> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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64 <param name="msp_input" value="split/sample_input.msp" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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65 <param name="split_type" value="num-chunks" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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66 <param name="num_chunks" value="2" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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67 <output_collection name="sample" type="list"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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68 <element name="chunk_0" file="split/num-chunks/chunk_0.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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69 <element name="chunk_1" file="split/num-chunks/chunk_1.msp" ftype="msp" compare="contains"/> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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70 </output_collection> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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71 </test> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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72 <test> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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73 <param name="msp_input" value="split/sample_input.msp" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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74 <param name="split_type" value="chunk-size" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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75 <param name="chunk_size" value="4" /> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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76 <output_collection name="sample" type="list"> |
169c72b2ce79
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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77 <element name="chunk_0" file="split/chunk-size/chunk_0.msp" ftype="msp" compare="contains"/> |
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78 <element name="chunk_1" file="split/chunk-size/chunk_1.msp" ftype="msp" compare="contains"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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79 <element name="chunk_2" file="split/chunk-size/chunk_2.msp" ftype="msp" compare="contains"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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80 </output_collection> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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81 </test> |
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82 </tests> |
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83 <help><![CDATA[ |
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84 Splitmsp handles input/output files in MSP format using the matchms.importing and matchms.exporting modules (https://matchms.readthedocs.io/en/latest/index.html). |
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85 |
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86 Please observe that the `num-chunks` method does not preserve the order of the elements as it uses a `round robin` distribution. |
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87 ]]></help> |
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88 <expand macro="citations"/> |
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89 </tool> |