Mercurial > repos > brinkmanlab > microbedb

annotate all_fasta.xml @ 9:b08b09342b92 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 8cc0daf7f7ce6a49483c9152bccd53d66a00f707"
author brinkmanlab
date Fri, 04 Dec 2020 20:07:41 +0000
parents 7c2f036e13a7
children 2f6ef3a184df
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1 <tool id="microbedb_all_fasta" name="MicrobeDB All FASTA" version="1.1" tool_type="manage_data" profile="18.09">
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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[
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16 sqlite3 -readonly '$db' < '$sql' > '$output'
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17 ]]></command>
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18 <configfiles>
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19 <configfile name="sql"><![CDATA[
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20 #import os.path
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21 SELECT json_object('data_tables', json_object(
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22 'all_fasta', json_group_array(json_object('value', unique_build_id, 'dbkey', dbkey, 'name', label, 'path', file_path))
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23 #if $builds
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24 ,'__dbkeys__', json_group_array(json_object('value', dbkey, 'name', label, 'len_path', ''))
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25 #end if
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26 )) FROM (
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27 SELECT (r.rep_accnum || '.' || r.rep_version) AS unique_build_id,
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28 (r.rep_accnum || '_' || r.rep_version) AS dbkey,
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29 (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version || ']') AS label,
6ad04790da12 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 86feecfffe799823fcbae7c56b04d4ef7c87117d"
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30 ('${os.path.dirname(str($db))}/' || genomeproject.gpv_directory || '/' || genomeproject.filename || '_genomic.fna') AS file_path
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31 FROM genomeproject JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome'
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32 WHERE genomeproject.file_types IS NOT NULL
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33 AND genomeproject.file_types LIKE '%.fna%'
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34 AND r.rep_type = 'chromosome'
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35 )
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36 ]]></configfile>
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37 </configfiles>
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38 <inputs>
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39 <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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40 <param name="builds" type="boolean" label="Add genomes to __dbkeys__" help="Add genomes to __dbkeys__ table, listing them at /api/genomes"/>
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41 </inputs>
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42 <outputs>
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43 <data name="output" format="data_manager_json" />
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44 </outputs>
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45 <tests>
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46 </tests>
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47 <help><![CDATA[
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48 Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories
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49 and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and
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50 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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51 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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52 for various large-scale comparative genomic analyses and a back-end for future microbial application design.
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53
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54 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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55 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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56 The MicrobeDB CVMFS repository is hosted at microbedb.brinkmanlab.ca.
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57 ]]></help>
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58 <citations>
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59 <citation type="doi">10.1093/bioinformatics/bts273</citation>
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60 </citations>
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61 </tool>