# HG changeset patch
# User iuc
# Date 1478094165 14400
# Node ID 0edbf19cf5eb6283403b0d007a1db8243b7c5f8f
# Parent  736d51130b41ec533890c4745f029b649f155c48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8

diff -r 736d51130b41 -r 0edbf19cf5eb README.md
--- a/README.md	Tue Sep 13 14:43:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-**Tool Information**
-
-- QUAST Tool v4.1:
-    + Release Date: May 2016
-    + URL: http://bioinf.spbau.ru/quast
-    + Source URL: https://downloads.sourceforge.net/project/quast/quast-4.1.tar.gz
-
------
-
-**QUAST Galaxy Wrapper Author and Contact Information**
-
-+ Delphine Lariviere
-+ Galaxy Team
-+ Email: delphine.lariviere@galaxyproject.org
-+ Nekrutenko's Lab, Pennsylvania State University, State College, PA, USA
-
-
-- From the wrapper of :
-    + Jacob Jablonski
-    + AAFC-MBB Team
-    + Email: mbb@agr.gc.ca
-    + Agriculture and Agri-foods Canada, Ottawa, ON, Canada
diff -r 736d51130b41 -r 0edbf19cf5eb README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Wed Nov 02 09:42:45 2016 -0400
@@ -0,0 +1,22 @@
+**Tool Information**
+
+- QUAST Tool v4.1:
+    + Release Date: May 2016
+    + URL: http://bioinf.spbau.ru/quast
+    + Source URL: https://downloads.sourceforge.net/project/quast/quast-4.1.tar.gz
+
+-----
+
+**QUAST Galaxy Wrapper Author and Contact Information**
+
++ Delphine Lariviere
++ Galaxy Team
++ Email: delphine.lariviere@galaxyproject.org
++ Nekrutenko's Lab, Pennsylvania State University, State College, PA, USA
+
+
+- From the wrapper of :
+    + Jacob Jablonski
+    + AAFC-MBB Team
+    + Email: mbb@agr.gc.ca
+    + Agriculture and Agri-foods Canada, Ottawa, ON, Canada
diff -r 736d51130b41 -r 0edbf19cf5eb quast.xml
--- a/quast.xml	Tue Sep 13 14:43:54 2016 -0400
+++ b/quast.xml	Wed Nov 02 09:42:45 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="quast" name="Quast" version="4.1" >
+<tool id="quast" name="Quast" version="4.1.1" >
     <description>Genome assembly Quality</description>
     <requirements>
         <requirement type="package" version="4.1">quast</requirement>
@@ -31,6 +31,9 @@
             --est-ref-size $input_size
         #end if
         --min-contig $min_contig
+        -l
+        #set names = ','.join( ['"'+str( $x.input.element_identifier)+'"' for $x in $files ])
+        $names
         --contig-thresholds $threshold_contig
         #for $k in $files:
             #if $k.type_file == "scaffold":
diff -r 736d51130b41 -r 0edbf19cf5eb test-data/Quast_report.tex
--- a/test-data/Quast_report.tex	Tue Sep 13 14:43:54 2016 -0400
+++ b/test-data/Quast_report.tex	Wed Nov 02 09:42:45 2016 -0400
@@ -5,7 +5,7 @@
 \caption{All statistics are based on contigs of size $\geq$ 500 bp, unless otherwise noted (e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).}
 \begin{tabular}{|l*{1}{|r}|}
 \hline
-Assembly & contigs\_1 \\ \hline
+Assembly & contigs\_1.fasta \\ \hline
 \# contigs ($\geq$ 0 bp) & 3 \\ \hline
 \# contigs ($\geq$ 1000 bp) & 3 \\ \hline
 Total length ($\geq$ 0 bp) & 6710 \\ \hline
diff -r 736d51130b41 -r 0edbf19cf5eb test-data/Quast_report.tsv
--- a/test-data/Quast_report.tsv	Tue Sep 13 14:43:54 2016 -0400
+++ b/test-data/Quast_report.tsv	Wed Nov 02 09:42:45 2016 -0400
@@ -1,4 +1,4 @@
-Assembly	contigs_1
+Assembly	contigs_1.fasta
 # contigs (>= 0 bp)	3
 # contigs (>= 1000 bp)	3
 Total length (>= 0 bp)	6710
diff -r 736d51130b41 -r 0edbf19cf5eb test-data/Quast_report.txt
--- a/test-data/Quast_report.txt	Tue Sep 13 14:43:54 2016 -0400
+++ b/test-data/Quast_report.txt	Wed Nov 02 09:42:45 2016 -0400
@@ -1,16 +1,16 @@
 All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
 
-Assembly                   contigs_1
-# contigs (>= 0 bp)        3        
-# contigs (>= 1000 bp)     3        
-Total length (>= 0 bp)     6710     
-Total length (>= 1000 bp)  6710     
-# contigs                  3        
-Largest contig             3980     
-Total length               6710     
-GC (%)                     51.28    
-N50                        3980     
-N75                        1610     
-L50                        1        
-L75                        2        
-# N's per 100 kbp          0.00     
+Assembly                   contigs_1.fasta
+# contigs (>= 0 bp)        3              
+# contigs (>= 1000 bp)     3              
+Total length (>= 0 bp)     6710           
+Total length (>= 1000 bp)  6710           
+# contigs                  3              
+Largest contig             3980           
+Total length               6710           
+GC (%)                     51.28          
+N50                        3980           
+N75                        1610           
+L50                        1              
+L75                        2              
+# N's per 100 kbp          0.00