diff data_manager/bracken_build_database.xml @ 0:911bb6c95bf8 draft default tip

"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit d0b060e7d9cc9fd89926dbc07fc93c8a1471b3fe-dirty"
author dfornika
date Thu, 24 Oct 2019 17:44:45 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bracken_build_database.xml	Thu Oct 24 17:44:45 2019 -0400
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+<?xml version="1.0"?>
+<tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5_galaxy0" profile="19.01">
+    <description>bracken database builder</description>
+    <requirements>
+        <requirement type="package" version="2.5">bracken</requirement>
+        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
+    </requirements>
+    <command>
+    <![CDATA[
+        python '$__tool_directory__/bracken_build_database.py'
+          '${out_file}'
+          --kraken-db '${kraken_db.fields.path}'
+          --threads \${GALAXY_SLOTS:-1}
+          --kmer-len ${kmer_len}
+          --read-len ${read_len}
+          --database-name '${database_name}'
+    ]]>
+    </command>
+    <inputs>
+        <param name="kraken_db" type="select">
+            <options from_data_table="kraken2_databases">
+                <validator type="no_options" message="No Kraken2 databases are available" />
+            </options>
+        </param>
+        <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" />
+        <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" />
+        <param name="database_name" type="text" label="Database Name" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="kraken_db" value="test_entry" />
+            <param name="database_name" value="database" />
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="test_db/database100mers.kmer_distrib" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+    </help>
+    <citations>
+        <citation type="doi">10.7717/peerj-cs.104</citation>
+    </citations>
+</tool>