# HG changeset patch
# User nick
# Date 1503555138 14400
# Node ID ffbdaa57d4c60895d6a0d01046f3c168f907a63a
# Parent  b4d7ec92b30f3c3a9f28b46cb1913f4bb08eaee5
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'b133d7a65a2371efa097a11ccf123587007e1662\n'-dirty

diff -r b4d7ec92b30f -r ffbdaa57d4c6 align_families.xml
--- a/align_families.xml	Thu Aug 24 02:01:11 2017 -0400
+++ b/align_families.xml	Thu Aug 24 02:12:18 2017 -0400
@@ -6,7 +6,7 @@
     <requirement type="package" version="0.7.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code">align_families.py --test --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
+  <command detect_errors="exit_code">align_families.py --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
diff -r b4d7ec92b30f -r ffbdaa57d4c6 correct_barcodes.xml
--- a/correct_barcodes.xml	Thu Aug 24 02:01:11 2017 -0400
+++ b/correct_barcodes.xml	Thu Aug 24 02:12:18 2017 -0400
@@ -11,7 +11,7 @@
   <command detect_errors="exit_code"><![CDATA[
     baralign.sh '$input' refdir barcodes.bam
     && samtools view -f 256 barcodes.bam
-    | correct.py --test --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa
+    | correct.py --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa
     | sort
     > '$output'
   ]]>
diff -r b4d7ec92b30f -r ffbdaa57d4c6 dunovo.xml
--- a/dunovo.xml	Thu Aug 24 02:01:11 2017 -0400
+++ b/dunovo.xml	Thu Aug 24 02:12:18 2017 -0400
@@ -6,7 +6,7 @@
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    dunovo.py --test --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input'
+    dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input'
     #if $keep_sscs:
       --sscs-file sscs.fa
     #end if