diff metaphlan2.xml @ 32:c941148c75c7 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty

--- a/metaphlan2.xml	Tue Feb 21 12:29:37 2017 -0500
+++ b/metaphlan2.xml	Wed Feb 22 03:49:35 2017 -0500
@@ -43,10 +43,11 @@
             --bowtie2_exe `which bowtie2`
 
             #if $db.db_selector == "cached"
-                #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data])
+                #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data])
                 #set $db_choice = $db.cached_db.value
-                --bowtie2db '$table[$db_choice]'
-                --mpa_pkl $table[$db_choice]".pkl"
+                #set $metadata = `ls $paths[$db_choice]/*.pkl`
+                --bowtie2db $metadata[:-4]
+                --mpa_pkl '$metadata'
             #else
                 --bowtie2db 'ref_db/ref_db'
                 --mpa_pkl 'ref_db/metadata.pkl'