--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.xml	Fri Oct 30 21:04:47 2020 +0000
@@ -0,0 +1,50 @@
+<tool id="microbedb_all_fasta" name="MicrobeDB All FASTA" version="1.0" tool_type="manage_data">
+    <description>Load all fasta files from MicrobeDB into the all_fasta data table</description>
+    <edam_topics>
+        <edam_topic>topic_3301</edam_topic>
+        <edam_topic>topic_0080</edam_topic>
+        <edam_topic>topic_0091</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_2422</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="3">sqlite</requirement>
+    </requirements>
+    <version_command>sqlite3 --version</version_command>
+    <command><![CDATA[
+        #import os.path
+        sqlite3 -readonly $db '.param set :basepath ${os.path.dirname($db)}' '.read $__tool_directory__/all_fasta.sql' > '$output';
+        #if $builds
+        sqlite3 -readonly $db < '$builds_sql'
+        #endif
+    ]]></command>
+    <configfiles>
+        <configfile name="builds_sql"><![CDATA[
+            #include $__tool_directory__/builds.sql
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="db" type="text" value="/cvmfs/microbedb.brinkmanlab.ca/microbedb.sqlite" label="Path" help="Absolute path to microbedb.sqlite on Galaxy host server"/>
+        <param name="builds" type="boolean" label="Append references to builds" help="Append genomes to Galaxies builds.txt, listing them at /api/genomes"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="data_manager_json" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+    Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories
+    and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and
+    archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction
+    with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource
+    for various large-scale comparative genomic analyses and a back-end for future microbial application design.
+
+    This tool populates the all_fasta table with the paths of the reference genomes included in MicrobeDB. MicrobeDB must first be manually loaded
+    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).
+    The MicrobeDB CVMFS repository is hosted at microbedb.brinkmanlab.ca.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts273</citation>
+    </citations>
+</tool>