diff data_manager/data_manager_cat.xml @ 0:f59e7e242bde draft

planemo upload commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_cat.xml	Sun Nov 24 21:54:57 2019 -0500
@@ -0,0 +1,44 @@
+<tool id="data_manager_cat" name="CAT DB" version="@VERSION@.0" tool_type="manage_data">
+    <description>Install a new CAT database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+#import json, os
+#set params = json.loads(open(str($out_file)).read())
+#set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
+mkdir -p $install_path &&
+python '${__tool_directory__}/data_manager_cat.py' --config_file '$out_file' --install_path '$install_path' 
+#if $db.src == 'download'
+    --db_url '$db_url'
+#end if
+    ]]></command>
+    <inputs>
+        <conditional name="db">
+            <param name="src" type="select" label="Download or Build DBs">
+                <option value="download">download</option>
+                <option value="build">build</option>
+            </param>
+            <when value="download">
+                <param name="db_url" type="text" label="DB rul at https://tbb.bio.uu.nl/bastiaan/CAT_prepare/"
+                     help="example: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz">
+                </param>
+            </when>
+            <when value="build">
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+This tool prepares reference data for CAT, the Contig Annotation Tool.  
+It can either download prebuilt reference data from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/
+or build new reference data using the CAT prepare application.
+    ]]></help>
+    <expand macro="citations" />
+</tool>