diff humann2_download_databases.xml @ 0:3d6f37e7e3a8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_download_databases.xml	Thu May 26 10:20:59 2016 -0400
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+<tool id="humann2_download_databases" name="Download" version="0.6.1">
+    <description>HUMAnN2 databases</description>
+
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+    humann2_databases --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        humann2_databases
+            --download $database_selector \${HUMANN2_DIR}/databases
+            
+            > $log
+    ]]></command>
+
+    <inputs>
+        <param name="database_selector" type="select" label="Database to download" help="">
+            <option value="chocophlan full">Nucleotide (ChocoPhlAn)</option>
+            <option value="uniref diamond">Protein (UniRef50)</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="log" label="${tool.name}: Log" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+
+Download HUMAnN2 databases is a tool to download needed nucleotide or protein databases. This tool must be run before using HUMAnN2.
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>
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