Mercurial > repos > brinkmanlab > microbedb

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