Mercurial > repos > devteam > kraken_translate

diff macros.xml @ 0:77ca66b1f5e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 23 Jul 2015 10:56:31 -0400
parents
children 475284b74179
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jul 23 10:56:31 2015 -0400
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.10.5">kraken</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code description="Tool exception" level="fatal" range="1:" />
+        </stdio>
+    </xml>
+    <xml name="version_command">
+        <version_command>export LC_ALL=C &amp;&amp; kraken --version</version_command>
+    </xml>
+    <xml name="input_database">
+        <param label="Select a Kraken database" name="kraken_database" type="select">
+            <options from_data_table="kraken_databases">
+                <validator message="No databases are available built-in" type="no_options" />
+            </options>
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
+        </citations>
+    </xml>
+    <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token>
+    <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token>
+</macros>
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