Mercurial > repos > rnateam > bctools

changeset 29:65103aba4e5f draft

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fix xml
author rnateam
date Thu, 17 Dec 2015 10:58:19 -0500
parents 3d608b751bc4
children 3239487fa9c5
files flexbar_dsc.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/flexbar_dsc.xml	Thu Dec 17 10:53:09 2015 -0500
+++ b/flexbar_dsc.xml	Thu Dec 17 10:58:19 2015 -0500
@@ -14,6 +14,8 @@
 
     <version_command>flexbar --version</version_command>
 
+    <command><![CDATA[
+
         flexbar
 
         --threads \${GALAXY_SLOTS:-1}
@@ -138,10 +140,7 @@
         --target FlexbarOutput &&
         for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done &&
         for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done
-
-
-
-    </command>
+    ]]></command>
 
 
     <inputs>
@@ -430,6 +429,7 @@
       -->
         <discover_datasets pattern="FlexbarOutput_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" />
         <!--<data format="txt" name="output" metadata_source="reads"/>-->
+        </collection>
     </outputs>