Mercurial > repos > devteam > data_manager_build_kraken_database

diff data_manager/kraken_database_builder.xml @ 3:404ba485ec01 draft

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Uploaded
author devteam
date Thu, 30 Apr 2015 16:16:05 -0400
parents cdef63d8a141
children 1de1817a8a57
line wrap: on
line diff
--- a/data_manager/kraken_database_builder.xml	Mon Apr 27 16:13:06 2015 -0400
+++ b/data_manager/kraken_database_builder.xml	Thu Apr 30 16:16:05 2015 -0400
@@ -21,7 +21,9 @@
             #end if
         #end for
         #for $fasta in $input_fasta:
-            kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta"  &&
+            #if str($fasta) != 'None':
+                kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta"  &&
+            #end if
         #end for
         kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len}  &&
         cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}"
@@ -45,4 +47,4 @@
     <citations>
         <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>