Mercurial > repos > iuc > data_manager_snpsift_dbnsfp
annotate data_manager/data_manager_snpsift_dbnsfp.xml @ 8:752439501b04 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit ad15c8e96a0633f1939266d63fd17978afa7d9b7
author | iuc |
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date | Thu, 09 Feb 2023 14:55:23 +0000 |
parents | e57f0b0bc73b |
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rev | line source |
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e57f0b0bc73b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
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1 <tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.1" tool_type="manage_data" profile="19.05"> |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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2 <description>Install a dbNSFP variant annotation database</description> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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3 <requirements> |
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d57ebdd39f0f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit dd0c7246fddad8f78b29c69909a307ed65f5e7f7
iuc
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4 <requirement type="package" version="0.8.3">pysam</requirement> |
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e57f0b0bc73b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
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5 <requirement type="package" version="2.7">python</requirement> |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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6 </requirements> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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7 <stdio> |
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47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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8 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> |
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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9 <exit_code range="1:" level="fatal" description="Error" /> |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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10 </stdio> |
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e57f0b0bc73b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
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11 <command> |
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47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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12 #import re |
6
e57f0b0bc73b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents:
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13 python '$__tool_directory__/data_manager_snpsift_dbnsfp.py' |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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14 #if $db.src == 'softgenetics': |
4
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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15 --softgenetics "$db.softgenetics_name" |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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16 #elif $db.src == 'history': |
4
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
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17 #if $db.snpsiftdbnsfp.is_of_type('snpsiftdbnsfp'): |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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18 #import os.path |
4
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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19 --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)" |
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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20 #else |
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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21 --dbnsfp_tabular "$db.snpsiftdbnsfp" |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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22 #end if |
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47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
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23 --db_name "$db.db_name" |
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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24 #if str($db.dbkey).strip() != '': |
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
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changeset
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25 --dbkey "$db.dbkey" |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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26 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?': |
4
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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diff
changeset
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27 --dbkey "$db.snpsiftdbnsfp.metadata.dbkey" |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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28 #end if |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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29 #end if |
4
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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30 "$out_file" |
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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31 </command> |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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32 <inputs> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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33 <conditional name="db"> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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34 <param name="src" type="select" label="Source for dbNSFP file"> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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35 <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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36 <option value="history">from your history</option> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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37 </param> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
diff
changeset
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38 <when value="softgenetics"> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
parents:
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39 <param name="softgenetics_name" type="text" value="" label="dbNSFP file name at softgenetics ftp site"> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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40 <help>Download From: ftp://dbnsfp.softgenetics.com/ |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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41 Enter the name of the database, e.g.: dbNSFPv3.0c.zip |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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42 </help> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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43 <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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44 </param> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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45 </when> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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46 <when value="history"> |
4
47f276ffcbfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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47 <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history" |
0
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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48 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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49 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database"> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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50 <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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51 <validator type="regex" message="No whitespace allowed">^\S*$</validator> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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52 </param> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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53 <param name="dbkey" type="text" value="hg19" optional="true" label="DBKEY to assign to data to this dbNSFP database" /> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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54 </when> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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55 </conditional> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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56 </inputs> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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57 |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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58 <outputs> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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59 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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60 </outputs> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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61 <tests> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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62 <test> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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63 <param name="src" value="history"/> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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64 <param name="snpsiftdbnsfp" value="test_nsfp.tsv" ftype="dbnsfp.tabular"/> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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65 <param name="dbkey" value="hg19"/> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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66 <param name="db_name" value="test_nsfp_tsv" /> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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67 <output name="out_file" file="test_nsfp.data_manager_json"/> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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68 </test> |
0e9e3bb5776a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
iuc
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69 </tests> |
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70 <help> |
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71 |
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72 This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_ |
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73 It populates data table: snpsift_dbnsfps |
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74 |
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75 .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP |
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76 .. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP |
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77 |
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78 Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions. |
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79 |
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80 </help> |
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81 <citations> |
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82 <citation type="doi">DOI: 10.1002/humu.21517</citation> |
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83 <citation type="doi">DOI: 10.1002/humu.22376</citation> |
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84 <citation type="doi">DOI: 10.1002/humu.22932</citation> |
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85 <citation type="doi">doi: 10.1093/hmg/ddu733</citation> |
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86 <citation type="doi">doi: 10.1093/nar/gku1206</citation> |
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87 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation> |
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88 </citations> |
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89 </tool> |
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90 |