Mercurial > repos > brinkmanlab > microbedb

comparison all_fasta.xml @ 7:6ad04790da12 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 86feecfffe799823fcbae7c56b04d4ef7c87117d"
author brinkmanlab
date Mon, 09 Nov 2020 23:15:23 +0000
parents 67447b96c3ff
children 7c2f036e13a7
comparison
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6:b7884a377566 7:6ad04790da12
11 <requirements> 11 <requirements>
12 <requirement type="package" version="3">sqlite</requirement> 12 <requirement type="package" version="3">sqlite</requirement>
13 </requirements> 13 </requirements>
14 <version_command>sqlite3 --version</version_command> 14 <version_command>sqlite3 --version</version_command>
15 <command><![CDATA[ 15 <command><![CDATA[
16 #import os.path 16 sqlite3 -readonly '$db' < '$sql' > '$output'
17 sqlite3 -readonly $db '.param set :basepath ${os.path.dirname(str($db))}' '.read $__tool_directory__/all_fasta.sql' > '$output'
18 #if $builds
19 && touch $__app__.config.builds_file_path && sqlite3 -readonly $db < '$builds_sql'
20 #end if
21 ]]></command> 17 ]]></command>
22 <configfiles> 18 <configfiles>
23 <configfile name="builds_sql"><![CDATA[ 19 <configfile name="sql"><![CDATA[
24 #include $__tool_directory__+"/builds.sql" 20 #import os.path
21 SELECT json_object('data_tables',
22 json_object('all_fasta', json_group_array(json_object('value', unique_build_id, 'dbkey', dbkey, 'name', label, 'path', file_path))),
23 #if $builds
24 json_object('__dbkeys__', json_group_array(json_object('value', dbkey, 'name', label, 'len_path', ''))),
25 #end if
26 ) FROM (
27 SELECT (r.rep_accnum || '.' || r.rep_version) AS unique_build_id,
28 (r.rep_accnum || '_' || r.rep_version) AS dbkey,
29 (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version || ']') AS label,
30 ('${os.path.dirname(str($db))}/' || genomeproject.gpv_directory || '/' || genomeproject.filename || '_genomic.fna') AS file_path
31 FROM genomeproject
32 JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome'
33 WHERE genomeproject.version_id = (SELECT version_id FROM version WHERE is_current == 1)
34 AND genomeproject.file_types IS NOT NULL
35 AND genomeproject.file_types LIKE '%.fna%'
36 AND r.rep_type = 'chromosome'
37 )
25 ]]></configfile> 38 ]]></configfile>
26 </configfiles> 39 </configfiles>
27 <inputs> 40 <inputs>
28 <param name="db" type="text" value="/cvmfs/microbedb.brinkmanlab.ca/microbedb.sqlite" label="Path" help="Absolute path to microbedb.sqlite on Galaxy host server"/> 41 <param name="db" type="text" value="/cvmfs/microbedb.brinkmanlab.ca/microbedb.sqlite" label="Path" help="Absolute path to microbedb.sqlite on Galaxy host server"/>
29 <param name="builds" type="boolean" label="Append references to builds" help="Append genomes to Galaxies builds.txt, listing them at /api/genomes"/> 42 <param name="builds" type="boolean" label="Add genomes to __dbkeys__" help="Add genomes to __dbkeys__ table, listing them at /api/genomes"/>
30 </inputs> 43 </inputs>
31 <outputs> 44 <outputs>
32 <data name="output" format="data_manager_json" /> 45 <data name="output" format="data_manager_json" />
33 </outputs> 46 </outputs>
34 <tests> 47 <tests>