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comparison all_fasta.xml @ 0:40d14d5c8125 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
author brinkmanlab
date Fri, 30 Oct 2020 21:04:47 +0000
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-1:000000000000 0:40d14d5c8125
1 <tool id="microbedb_all_fasta" name="MicrobeDB All FASTA" version="1.0" tool_type="manage_data">
2 <description>Load all fasta files from MicrobeDB into the all_fasta data table</description>
3 <edam_topics>
4 <edam_topic>topic_3301</edam_topic>
5 <edam_topic>topic_0080</edam_topic>
6 <edam_topic>topic_0091</edam_topic>
7 </edam_topics>
8 <edam_operations>
9 <edam_operation>operation_2422</edam_operation>
10 </edam_operations>
11 <requirements>
12 <requirement type="package" version="3">sqlite</requirement>
13 </requirements>
14 <version_command>sqlite3 --version</version_command>
15 <command><![CDATA[
16 #import os.path
17 sqlite3 -readonly $db '.param set :basepath ${os.path.dirname($db)}' '.read $__tool_directory__/all_fasta.sql' > '$output';
18 #if $builds
19 sqlite3 -readonly $db < '$builds_sql'
20 #endif
21 ]]></command>
22 <configfiles>
23 <configfile name="builds_sql"><![CDATA[
24 #include $__tool_directory__/builds.sql
25 ]]></configfile>
26 </configfiles>
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"/>
29 <param name="builds" type="boolean" label="Append references to builds" help="Append genomes to Galaxies builds.txt, listing them at /api/genomes"/>
30 </inputs>
31 <outputs>
32 <data name="output" format="data_manager_json" />
33 </outputs>
34 <tests>
35 </tests>
36 <help><![CDATA[
37 Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories
38 and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and
39 archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction
40 with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource
41 for various large-scale comparative genomic analyses and a back-end for future microbial application design.
42
43 This tool populates the all_fasta table with the paths of the reference genomes included in MicrobeDB. MicrobeDB must first be manually loaded
44 onto the Galaxy filesystem. The easiest way of doing that is mounting it using the [CVMFS client](https://cvmfs.readthedocs.io/en/stable/cpt-quickstart.html).
45 The MicrobeDB CVMFS repository is hosted at microbedb.brinkmanlab.ca.
46 ]]></help>
47 <citations>
48 <citation type="doi">10.1093/bioinformatics/bts273</citation>
49 </citations>
50 </tool>