diff kraken.xml @ 7:658d47fd33e3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 659d4506dad485d853a91a6a6f8bed1e3c56e204
author iuc
date Thu, 13 Sep 2018 09:44:31 -0400
parents 2fdac3e78553
children 8ba2174315aa
line wrap: on
line diff
--- a/kraken.xml	Mon Aug 07 17:29:06 2017 -0400
+++ b/kraken.xml	Thu Sep 13 09:44:31 2018 -0400
@@ -37,7 +37,7 @@
                 #else:
                     --fasta-input
                 #end if
-                "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"
+                '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
                 ${single_paired.check_names}
             #else:
                 #if $single_paired.input_sequences.is_of_type('fastq')
@@ -49,13 +49,13 @@
             #end if
 
             #if $split_reads:
-                --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
+                --classified-out '${classified_out}' --unclassified-out '${unclassified_out}'
             #end if
 
             ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3
 
-            > "${output}"
-            ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
+            > '${output}'
+            ##kraken-translate --db '${kraken_database.fields.name}' '${output}' > '${translated}'
     ]]></command>
     <inputs>
         <conditional name="single_paired">