diff correct_barcodes.xml @ 17:a34e074e4818 draft

correct.py wrapper fix

--- a/correct_barcodes.xml	Wed Oct 25 19:06:12 2017 -0400
+++ b/correct_barcodes.xml	Fri Oct 27 12:39:26 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6.1">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="2.2.5">bowtie2</requirement>
@@ -8,12 +8,14 @@
     <requirement type="package" version="2.0.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
+  <version_command>correct.py --version</version_command>
   <command detect_errors="exit_code"><![CDATA[
-    baralign.sh '$input' refdir
-    | samtools view -S -f 256 -
+    baralign.sh '$input' refdir correct.sam
+    && samtools view -S -f 256 correct.sam
     | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa
-    | sort
-    > '$output'
+      > families.corrected.tsv
+    && sort families.corrected.tsv
+      > '$output'
   ]]>
   </command>
   <inputs>