# HG changeset patch
# User nml
# Date 1470686216 14400
# Node ID 35cb17bd8bf9fa59c2a40f8e0477235e3ce3591b
# Parent  6dff6ed33cd7c58eb7a8a1d72995e4056d9a04a5
planemo upload commit ba4e93c036a072d6aac883bc1aba55e26256498c

diff -r 6dff6ed33cd7 -r 35cb17bd8bf9 CHANGE
--- a/CHANGE	Wed Jul 06 16:01:02 2016 -0400
+++ b/CHANGE	Mon Aug 08 15:56:56 2016 -0400
@@ -1,6 +1,10 @@
+1.4
+===
+ - Supports SPAdes 3.9
+ - CHANGE : Several minor bugs.
 1.3
 ===
- - Supports SPades 3.8
+ - Supports SPAdes 3.8
  - CHANGE: Improved running time and RAM consumption.
 
 1.2
diff -r 6dff6ed33cd7 -r 35cb17bd8bf9 output_dir/input_dataset.yaml
--- a/output_dir/input_dataset.yaml	Wed Jul 06 16:01:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-- left reads: [/tmp/tmpwz6C_M/files/000/dataset_15.dat]
-  orientation: fr
-  right reads: [/tmp/tmpwz6C_M/files/000/dataset_16.dat]
-  type: paired-end
diff -r 6dff6ed33cd7 -r 35cb17bd8bf9 spades.xml
--- a/spades.xml	Wed Jul 06 16:01:02 2016 -0400
+++ b/spades.xml	Mon Aug 08 15:56:56 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="spades" name="spades" version="1.3.2">
+<tool id="spades" name="spades" version="1.4">
   <description>SPAdes genome assembler for regular and single-cell projects</description>
   <requirements>
-    <requirement type="package" version="3.8.0">spades</requirement>
+    <requirement type="package" version="3.9.0">spades</requirement>
   </requirements>
   <command interpreter="perl">spades.pl 
     $out_contigs 
@@ -25,7 +25,7 @@
     $careful
     -t \${GALAXY_SLOTS:-16}
 
-    #if str($kmer_choice.auto_kmer_choice) == 'False':
+    #if not $kmer_choice.auto_kmer_choice:
     -k "$kmer_choice.kmers"    
     #else
 
@@ -249,7 +249,7 @@
 
 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
 
-This wrapper runs SPAdes 3.8, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. 
+This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. 
 
 **License**
 
diff -r 6dff6ed33cd7 -r 35cb17bd8bf9 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 06 16:01:02 2016 -0400
+++ b/tool_dependencies.xml	Mon Aug 08 15:56:56 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="spades" version="3.8.0">
-        <repository changeset_revision="c9eab59c0bc2" name="package_spades_3_8_0" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="spades" version="3.9.0">
+        <repository changeset_revision="d8c8c3dc8f9a" name="package_spades_3_9_0" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>