Mercurial > repos > bebatut > metaphlan2

changeset 36:969ae2fd4c84 draft

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Uploaded
author bebatut
date Thu, 23 Feb 2017 08:00:20 -0500
parents c312685a4b26
children e7ed163633e1
files metaphlan2.xml
diffstat 1 files changed, 4 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/metaphlan2.xml	Wed Feb 22 09:27:24 2017 -0500
+++ b/metaphlan2.xml	Thu Feb 23 08:00:20 2017 -0500
@@ -42,10 +42,9 @@
             --bowtie2_exe `which bowtie2`
 
             #if $db.db_selector == "cached"
-                #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data])
-                #set $db_choice = $db.cached_db.value
-                --bowtie2db `ls $paths[$db_choice]/*.pkl | sed 's/\(.*\)\..*/\1/'`
-                --mpa_pkl `ls $paths[$db_choice]/*.pkl`
+                #set $path = ${db.cached_db.fields.path}
+                --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'`
+                --mpa_pkl `ls $path/*.pkl`
             #else
                 --bowtie2db 'ref_db/ref_db'
                 --mpa_pkl 'ref_db/metadata.pkl'
@@ -85,7 +84,7 @@
             </param>
             <when value="cached">
                 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
-                <options from_data_table="metaphlan2_database" />
+                    <options from_data_table="metaphlan2_database" />
                 </param>
             </when>
             <when value="history">