Mercurial > repos > dfornika > kraken2

diff macros.xml @ 0:a77e88d426d9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
author dfornika
date Fri, 01 Mar 2019 12:43:26 -0500
parents
children 7932d09da19b
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Mar 01 12:43:26 2019 -0500
@@ -0,0 +1,15 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.0.7_beta</token>
+    <token name="@INTYPES@">
+        fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz
+    </token>
+    <xml name="input_database">
+        <param label="Select a Kraken2 database" name="kraken2_database" type="select">
+            <options from_data_table="kraken2_databases">
+                <validator message="No Kraken2 database is available" type="no_options" />
+            </options>
+        </param>
+    </xml>
+    <token name="@SET_DATABASE_PATH@">if [ -d '${kraken2_database.fields.path}/${kraken2_database.fields.name}' ]; then export KRAKEN2_DEFAULT_DB='${kraken2_database.fields.path}/${kraken2_database.fields.name}'; else export KRAKEN2_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
+    <token name="@INPUT_DATABASE@">--db "\$KRAKEN2_DEFAULT_DB"</token>
+</macros>