Mercurial > repos > brinkmanlab > microbedb

comparison all_fasta.xml @ 2:258826db8291 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 668759e2fc5d53432092d7c1395b402385733171"
author brinkmanlab
date Fri, 06 Nov 2020 21:26:52 +0000
parents 40d14d5c8125
children 7b432c6ff465
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1:5e94458c2dde 2:258826db8291
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 #import os.path
17 sqlite3 -readonly $db '.param set :basepath ${os.path.dirname($db)}' '.read $__tool_directory__/all_fasta.sql' > '$output'; 17 sqlite3 -readonly $db '.param set :basepath ${os.path.dirname(str($db))}' '.read $__tool_directory__/all_fasta.sql' > '$output';
18 #if $builds 18 #if $builds
19 sqlite3 -readonly $db < '$builds_sql' 19 sqlite3 -readonly $db < '$builds_sql'
20 #endif 20 #end if
21 ]]></command> 21 ]]></command>
22 <configfiles> 22 <configfiles>
23 <configfile name="builds_sql"><![CDATA[ 23 <configfile name="builds_sql"><![CDATA[
24 #include $__tool_directory__/builds.sql 24 #include $__tool_directory__+"/builds.sql"
25 ]]></configfile> 25 ]]></configfile>
26 </configfiles> 26 </configfiles>
27 <inputs> 27 <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"/> 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"/>
29 <param name="builds" type="boolean" label="Append references to builds" help="Append genomes to Galaxies builds.txt, listing them at /api/genomes"/> 29 <param name="builds" type="boolean" label="Append references to builds" help="Append genomes to Galaxies builds.txt, listing them at /api/genomes"/>