changeset 12:33a5a81e10ee draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 659d4506dad485d853a91a6a6f8bed1e3c56e204

--- a/kraken.xml	Mon Aug 07 17:26:55 2017 -0400
+++ b/kraken.xml	Thu Sep 13 09:43:38 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">

--- a/macros.xml	Mon Aug 07 17:26:55 2017 -0400
+++ b/macros.xml	Thu Sep 13 09:43:38 2018 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">1.2.3</token>
+    <token name="@WRAPPER_VERSION@">1.2.4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
@@ -23,6 +23,6 @@
             <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
         </citations>
     </xml>
-    <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token>
-    <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token>
+    <token name="@INPUT_DATABASE@">--db '${kraken_database.fields.name}'</token>
+    <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH='${kraken_database.fields.path}'</token>
 </macros>