Mercurial > repos > iuc > data_manager_humann2_database_downloader

diff data_manager/data_manager_humann2_download.xml @ 0:048593e41359 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
author iuc
date Sun, 12 Mar 2017 14:33:34 -0400
parents
children 1316375a8cbb
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_humann2_download.xml	Sun Mar 12 14:33:34 2017 -0400
@@ -0,0 +1,56 @@
+<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="0.9.9" tool_type="manage_data">
+    <description>Download HUMAnN2 database</description>
+    <requirements>
+        <requirement type="package" version="0.9.9">humann2</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python">
+        data_manager_humann2_download.py
+            --database '$db.database'
+            --build '$db.build'
+            '${out_file}'
+    </command>
+    <inputs>
+        <conditional name="db">
+            <param name="database" type="select" label="Type of database to download">
+                <option value="chocophlan" selected="true">Nucleotide database</option>
+                <option value="uniref">Protein database</option>
+            </param>
+            <when value="chocophlan">
+                <param name="build" type="select" label="Build for nucleotide database">
+                    <option value="full" selected="true">Full</option>
+                    <option value="DEMO">Demo</option>
+                </param>
+            </when>
+            <when value="uniref">
+                <param name="build" type="select" label="Build for protein database">
+                    <option value="uniref50_diamond">Full UniRef50</option>
+                    <option value="uniref50_ec_filtered_diamond">EC-filtered UniRef50</option>
+                    <option value="uniref50_GO_filtered_rapsearch2">GO filtered UniRef50 for rapsearch2</option>
+                    <option value="uniref90_diamond" selected="true">Full UniRef50</option>
+                    <option value="uniref90_ec_filtered_diamond">EC-filtered UniRef90</option>
+                    <option value="DEMO_diamond">Demo</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+
+This tool downloads the HUMAnN2 databases.
+
+`Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+
+    </help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1003153</citation>
+        <yield />
+    </citations>
+</tool>