# HG changeset patch
# User nick
# Date 1510324409 18000
# Node ID e7b88ffb8294d7ee76a5a43b786e08a92bbba8ea
# Parent  23f5d931669441a6c2d0af040b6e6afec8084357
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty

diff -r 23f5d9316694 -r e7b88ffb8294 align_families.xml
--- a/align_families.xml	Thu Nov 02 16:24:48 2017 -0400
+++ b/align_families.xml	Fri Nov 10 09:33:29 2017 -0500
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="2.0.8">
+<tool id="align_families" name="Du Novo: Align families" version="2.0.9">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="2.0.8">dunovo</requirement>
+    <requirement type="package" version="2.0.9">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <version_command>align_families.py --version</version_command>
-  <command detect_errors="exit_code">align_families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
+  <version_command>align-families.py --version</version_command>
+  <command detect_errors="exit_code">align-families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
diff -r 23f5d9316694 -r e7b88ffb8294 correct_barcodes.xml
--- a/correct_barcodes.xml	Thu Nov 02 16:24:48 2017 -0400
+++ b/correct_barcodes.xml	Fri Nov 10 09:33:29 2017 -0500
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.8">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.9">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="2.2.5">bowtie2</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
     <requirement type="package" version="1.10">networkx</requirement>
-    <requirement type="package" version="2.0.8">dunovo</requirement>
+    <requirement type="package" version="2.0.9">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <version_command>correct.py --version</version_command>
diff -r 23f5d9316694 -r e7b88ffb8294 dunovo.xml
--- a/dunovo.xml	Thu Nov 02 16:24:48 2017 -0400
+++ b/dunovo.xml	Fri Nov 10 09:33:29 2017 -0500
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
-<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.8">
+<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.9">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="2.0.8">dunovo</requirement>
+    <requirement type="package" version="2.0.9">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <version_command>dunovo.py --version</version_command>
+  <version_command>make-consensi.py --version</version_command>
   <command detect_errors="exit_code">
-    dunovo.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'
+    make-consensi.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'
     #if $keep_sscs:
       --sscs1 '$sscs1' --sscs2 '$sscs2'
     #end if
diff -r 23f5d9316694 -r e7b88ffb8294 make_families.xml
--- a/make_families.xml	Thu Nov 02 16:24:48 2017 -0400
+++ b/make_families.xml	Fri Nov 10 09:33:29 2017 -0500
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="2.0.8">
+<tool id="make_families" name="Du Novo: Make families" version="2.0.9">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="2.0.8">dunovo</requirement>
+    <requirement type="package" version="2.0.9">dunovo</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
-  <version_command>dunovo.py --version</version_command>
+  <version_command>make-consensi.py --version</version_command>
   <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' &gt; '$output'
   </command>
   <inputs>
diff -r 23f5d9316694 -r e7b88ffb8294 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 02 16:24:48 2017 -0400
+++ b/tool_dependencies.xml	Fri Nov 10 09:33:29 2017 -0500
@@ -12,10 +12,10 @@
   <package name="networkx" version="1.10">
     <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="dunovo" version="2.0.8">
+  <package name="dunovo" version="2.0.9">
     <install version="1.0">
       <actions>
-        <action sha256sum="4c105e29eff271b9e32f12c5d2862b717ba960981f4820dae26e159e2a0ed33d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.8.tar.gz</action>
+        <action sha256sum="6f5295b8eae0e161ee3bd28829ca140657743c695624ffc7f467f13eab2c547c" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.9.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>