Mercurial > repos > computational-metabolomics > sirius_csifingerid
annotate sirius_csifingerid.xml @ 9:8dac4cef0a22 draft default tip
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
| author | computational-metabolomics |
|---|---|
| date | Wed, 16 Feb 2022 16:11:55 +0000 |
| parents | 7b9c17738db8 |
| children |
| rev | line source |
|---|---|
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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1 <tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID" |
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9
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
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2 version="4.9.8+galaxy4" profile="19.05"> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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3 <description>is used to identify metabolites using single and |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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4 tandem mass spectrometry</description> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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5 <requirements> |
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4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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6 <requirement type="package" version="4.9.8"> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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7 sirius-csifingerid</requirement> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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8 </requirements> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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9 <command detect_errors="exit_code"> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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10 <![CDATA[ |
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8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
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11 export _JAVA_OPTIONS=-Duser.home=$__new_file_path__ && |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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12 python '$__tool_directory__/sirius_csifingerid.py' |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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13 --input_pth '$input' |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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14 --database $database |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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15 --profile $profile |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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16 --candidates $candidates |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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17 --ppm_max $ppm_max |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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18 --polarity $polarity |
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96b077221201
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a"
computational-metabolomics
parents:
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19 --out_dir $__new_file_path__ |
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4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
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20 --canopus_result_pth canopus_all_summary.tsv |
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4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
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21 --annotations_result_pth annotations_all_summary.tsv |
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8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
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22 --all_structures_result_pth structures_all_summary.tsv |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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23 --cores_top_level 1 |
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8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
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24 --cores_sirius \${GALAXY_SLOTS:-4} |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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25 --meta_select_col $meta_select_col |
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4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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26 --min_MSMS_peaks $min_MSMS_peaks |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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27 --schema $schema |
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96b077221201
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a"
computational-metabolomics
parents:
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28 --temp_dir $__new_file_path__ |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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29 |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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30 #if $adducts_cond.adducts_selector == 'select': |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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31 #for $a in $adducts_cond.adducts |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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32 --adducts $a |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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33 #end for |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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34 #elif $adducts_cond.adducts_selector == 'all': |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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35 #if $polarity == 'positive': |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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36 --adducts [M+H]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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37 --adducts [M+NH4]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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38 --adducts [M+Na]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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39 --adducts [M+K]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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40 --adducts [M+CH3OH+H]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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41 --adducts [M+ACN+H]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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42 --adducts [M+ACN+Na]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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43 --adducts [M+2ACN+H]+ |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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44 #elif $polarity == 'negative': |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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45 --adducts [M-H]- |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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46 --adducts [M+Cl]- |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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47 --adducts [M+HCOO]- |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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48 --adducts [M+CH3COO]- |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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49 #end if |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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50 #end if |
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856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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51 |
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4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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52 |
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4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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53 |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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54 ]]></command> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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55 <inputs> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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56 <param name="input" argument="--input_pth" type="data" format="msp" |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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57 label="MSP file (output from Create MSP tool)" /> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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58 <param argument="--database" type="select" |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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59 label="Select SIRIUS-CSI:FingerID Database" > |
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4
8fb51147d15e
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
computational-metabolomics
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60 <option value="PUBCHEM" >PubChem</option> |
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8fb51147d15e
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
computational-metabolomics
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61 <option value="HMDB">HMDB</option> |
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8fb51147d15e
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
computational-metabolomics
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62 <option value="KEGG">KEGG</option> |
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8fb51147d15e
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
computational-metabolomics
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63 <option value="KNAPSACK">KNApSAcK</option> |
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8fb51147d15e
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
computational-metabolomics
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64 <option value="BIOCYC">BioCyc</option> |
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8fb51147d15e
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
computational-metabolomics
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65 <option selected="true" value="BIO">Bio (all biological)</option> |
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8fb51147d15e
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
computational-metabolomics
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66 <option value="ALL">All (use all databases)</option> |
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0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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67 </param> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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68 <param argument="--ppm_max" type="integer" value="10" min="0" |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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69 label="Mass deviation of the fragment peaks in ppm" /> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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70 <param argument="--candidates" type="integer" value="5" min="1" |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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71 label="Maximum number of candidates in the output" /> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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72 <param argument="--polarity" type="select" label="Ion mode" > |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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73 <option value="positive" selected="true">Positive</option> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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74 <option value="negative">Negative</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
75 </param> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
76 <param argument="--profile" type="select" label="Analysis used" > |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
77 <option value="orbitrap" selected="true">Orbitrap</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
78 <option value="qtof">qTOF</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
79 <option value="fticr">FT-ICR</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
80 </param> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
81 <param argument="--schema" type="select" label="Schema" |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
82 help="Schema used for the MSP file (auto will try to |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
83 determine the schema automatically)"> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
84 <option value="auto" selected="True">Auto</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
85 <option value="msp" >Generic MSP</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
86 <option value="massbank">MassBank</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
87 </param> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
88 <param argument="--meta_select_col" type="select" |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
89 label="Choose how additional metadata columns are extracted" |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
90 help="The SIRIUS-CSI:Fingerid output can have additional |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
91 metadata columns added; these can be either extracted from all |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
92 MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
93 parameters. Additionally, columns can be added from the 'Name' |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
94 or 'RECORD_TITLE' parameters by splitting on | and : e.g. |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
95 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
96 xcms_grp_id columns"> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
97 <option value="name" selected="true"> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
98 Extra metadata columns from the Name or RECORD_TITLE</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
99 <option value="name_split" > |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
100 Extra metadata columns from the Name or |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
101 RECORD_TITLE (each column is split on "|" and ":" ) </option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
102 <option value="all"> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
103 Extra metadata columns from all MSP parameters</option> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
104 </param> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
changeset
|
105 <param argument="--min_MSMS_peaks" type="integer" min="0" value="0" |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
106 label="Minimum number of MS/MS peaks"/> |
|
2
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
107 |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
108 <conditional name="adducts_cond"> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
109 <param name="adducts_selector" type="select" label="How to handle adducts" |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
110 help="Choose whether to include a suspect list"> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
111 <option value="msp" selected="True">Use adducts defined in MSP file</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
112 <option value="select" >Select from list of adducts</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
113 <option value="all" >Use pre-selected adducts for either pos or neg ionisation mode</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
114 </param> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
115 <when value="msp"> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
116 </when> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
117 <when value="select"> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
118 <param argument="--adducts" label="Select adducts" |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
119 type="select" help="" multiple="true" display="checkboxes"> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
120 <option value="[M+H]+" selected="True">[M+H]+ 1.007276</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
121 <option value="[M+NH4]+">[M+NH4]+ 18.034374</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
122 <option value="[M+Na]+">[M+Na]+ 22.989218</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
123 <option value="[M+K]+">[M+K]+ 38.963158</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
124 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+ 33.033489</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
125 <option value="[M+ACN+H]+">[M+ACN+H]+ 42.033823</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
126 <option value="[M+ACN+Na]+">[M+ACN+Na]+ 64.015765</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
127 <option value="[M+2ACN+H]+">[M+2ACN+H]+ 83.06037</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
128 <option value="[M-H]-" >[M-H]- -1.007276</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
129 <option value="[M+Cl]-">[M+Cl]- 34.969402</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
130 <option value="[M+HCOO]-">[M+HCOO]- 44.99819</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
131 <option value="[M+CH3COO]-">[M+CH3COO]- 59.01385</option> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
132 </param> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
133 </when> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
134 <when value="all"> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
135 </when> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
136 </conditional> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
changeset
|
137 |
|
9
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
8
diff
changeset
|
138 <!-- <param argument="--rank_filter" type="integer" value="0"--> |
|
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
8
diff
changeset
|
139 <!-- label="Only show the top ranked annotations less than or equal--> |
|
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
8
diff
changeset
|
140 <!-- to this value (default to show all annotations)"/>--> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
changeset
|
141 |
|
9
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
8
diff
changeset
|
142 <!-- <param argument="--confidence_filter" type="float" value="0"--> |
|
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
8
diff
changeset
|
143 <!-- label="Only show annotations greater than or or equal--> |
|
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
8
diff
changeset
|
144 <!-- to this value (default to show all annotations)"/>--> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
changeset
|
145 |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
146 </inputs> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
changeset
|
147 <outputs> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
changeset
|
148 <data name="canopus_results" format="tsv" label="${tool.name} on ${on_string}: CANOPUS" |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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2
diff
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149 from_work_dir="canopus_all_summary.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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diff
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|
150 <data name="annotation_results" format="tsv" label="${tool.name} on ${on_string}: Annotations" |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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|
151 from_work_dir="annotations_all_summary.tsv"/> |
|
9
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
parents:
8
diff
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152 <data name="structure_results" format="tsv" label="${tool.name} on ${on_string}: All structures" |
|
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
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8
diff
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|
153 from_work_dir="structures_all_summary.tsv"/> |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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154 </outputs> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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155 <tests> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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156 <test> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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157 <!-- Test "massbank" style data format --> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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158 <param name="input" value="ML006801.txt" ftype="msp"/> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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159 <output name="annotation_results" file="annotation_ML006801.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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160 <output name="canopus_results" file="canopus_ML006801.tsv"/> |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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|
161 </test> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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162 <test> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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163 <!-- Test "generic format" style data format --> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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164 <param name="input" value="generic.msp" ftype="msp"/> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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165 <output name="annotation_results" file="annotation_generic.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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166 <output name="canopus_results" file="canopus_generic.tsv"/> |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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|
167 </test> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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168 <test> |
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9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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169 <!-- Test for glucose (qtof) MassBank data format --> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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|
170 <param name="input" value="RP022611.txt" ftype="msp"/> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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171 <param name="profile" value="qtof"/> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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|
172 <output name="annotation_results" file="annotation_RP022611_result.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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173 <output name="canopus_results" file="canopus_RP022611_result.tsv"/> |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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174 </test> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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175 <test> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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|
176 <!-- Test for glucose (q-exactive) GNPS, MoNA data format (and test canopus)--> |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
diff
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177 <param name="input" value="CCMSLIB00000578155.msp" ftype="msp"/> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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178 <param name="profile" value="orbitrap"/> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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|
179 <output name="annotation_results" file="annotation_CCMSLIB00000578155_result.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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diff
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180 <output name="canopus_results" file="canopus_CCMSLIB00000578155_result.tsv"/> |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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181 </test> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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diff
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182 <test> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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183 <!-- Test invalid adduct --> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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diff
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184 <param name="input" value="invalid_adduct.msp" ftype="msp"/> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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|
185 <output name="annotation_results" file="annotation_invalid_adduct_result.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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2
diff
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186 <output name="canopus_results" file="canopus_invalid_adduct_result.tsv"/> |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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187 </test> |
|
2
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
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|
188 <test> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
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|
189 <!-- Test all adducts --> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
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|
190 <param name="input" value="RP022611.txt" ftype="msp"/> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
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|
191 <param name="profile" value="qtof"/> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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diff
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|
192 <param name="polarity" value="negative"/> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
1
diff
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193 <conditional name="adducts_cond"> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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1
diff
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194 <param name="adducts_selector" value="all"/> |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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diff
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195 </conditional> |
|
3
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
parents:
2
diff
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|
196 <output name="annotation_results" file="annotation_RP022611_result_all_adducts.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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diff
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197 <output name="canopus_results" file="canopus_RP022611_result_all_adducts.tsv"/> |
|
4cbfd3d0a4c4
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac"
computational-metabolomics
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198 </test> |
|
9
8dac4cef0a22
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"
computational-metabolomics
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diff
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|
199 |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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200 </tests> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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201 <help> |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
parents:
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202 ---------------- |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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203 SIRIUS-FingerID |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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204 ---------------- |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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205 |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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206 Description |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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207 ----------- |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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208 |
|
2
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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diff
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209 SIRIUS is a java-based software framework for discovering a landscape of |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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210 de-novo identification of metabolites using single and tandem mass |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
parents:
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diff
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211 spectrometry. SIRIUS uses isotope pattern analysis for detecting the |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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diff
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212 molecular formula and further analyses the fragmentation pattern of a |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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213 compound using fragmentation trees. Website: |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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diff
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214 https://bio.informatik.uni-jena.de/software/sirius/ |
|
856b3761277d
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"
computational-metabolomics
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215 |
|
0
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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|
216 |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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|
217 Parameters |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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218 ---------- |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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219 |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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|
220 **\1. MSP file** |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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|
221 |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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222 MSP file created using *Create MSP* tool |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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223 |
|
9e6bf7278257
"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"
computational-metabolomics
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224 **\2. Select SIRIUS-CSI:FingerID Databases** |
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225 |
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226 The following databases are available: |
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227 |
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228 * PubChem |
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229 |
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230 * HMDB |
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231 |
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232 * KEGG |
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233 |
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234 * KNApSAcK |
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235 |
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236 * BioCyc |
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237 |
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3
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238 * Bio (default in CLI) |
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239 |
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240 * All |
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0
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241 |
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242 **\3. Mass deviation of the fragment peaks in ppm** |
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243 |
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244 Allowed mass deviation of the fragment peaks. |
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245 |
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246 **\4. The maximum number of candidates in the output** |
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247 |
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248 Set the top X candidates to return. |
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249 |
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250 **\5. Ion mode** |
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251 |
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252 * Positive |
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253 |
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254 * Negative |
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255 |
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256 **\6. Analysis used** |
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257 |
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258 * Orbitrap |
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259 |
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260 * qTOF |
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261 |
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262 * FT-ICR |
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263 |
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264 If you want to analyze spectra measured with Orbitrap or FT-ICR, you should |
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265 specify the appropriate analysis profile. A profile is a set of configuration |
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266 options and scoring functions SIRIUS 3 will use for its analysis. For example, |
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267 the Orbitrap and FT-ICR profiles have tighter constraints for the allowed mass |
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268 deviation but do not rely so much on the intensity of isotope peaks. |
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269 |
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270 |
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271 Developers and contributors |
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272 --------------------------- |
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273 |
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274 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)** |
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275 - **Thomas N Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)** |
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276 - **Simon Bray (sbray@informatik.uni-freiburg.de) - University of Freiburg (Germany)** |
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277 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)** |
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278 |
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279 </help> |
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280 <citations> |
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281 <citation type="doi">10.1073/pnas.1509788112</citation> |
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282 <citation type="doi">10.1093/bioinformatics/btu275</citation> |
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283 </citations> |
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284 </tool> |