# HG changeset patch
# User iuc
# Date 1478250375 14400
# Node ID 2f581f956e1c131c406a3af9897662d96561352c
# Parent  0edbf19cf5eb6283403b0d007a1db8243b7c5f8f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 930a43568ac0d4d32dde38a56fbb0b826f8f591b

diff -r 0edbf19cf5eb -r 2f581f956e1c quast.xml
--- a/quast.xml	Wed Nov 02 09:42:45 2016 -0400
+++ b/quast.xml	Fri Nov 04 05:06:15 2016 -0400
@@ -11,6 +11,7 @@
     </stdio>
     <command>
     <![CDATA[
+        #import re
         quast
         -o outputdir
         #if $gene_selection == "eukaryote":
@@ -32,7 +33,8 @@
         #end if
         --min-contig $min_contig
         -l
-        #set names = ','.join( ['"'+str( $x.input.element_identifier)+'"' for $x in $files ])
+        #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ])
+        
         $names
         --contig-thresholds $threshold_contig
         #for $k in $files:
diff -r 0edbf19cf5eb -r 2f581f956e1c test-data/Quast_report.tex
--- a/test-data/Quast_report.tex	Wed Nov 02 09:42:45 2016 -0400
+++ b/test-data/Quast_report.tex	Fri Nov 04 05:06:15 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.fasta \\ \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 0edbf19cf5eb -r 2f581f956e1c test-data/Quast_report.tsv
--- a/test-data/Quast_report.tsv	Wed Nov 02 09:42:45 2016 -0400
+++ b/test-data/Quast_report.tsv	Fri Nov 04 05:06:15 2016 -0400
@@ -1,4 +1,4 @@
-Assembly	contigs_1.fasta
+Assembly	contigs_1_fasta
 # contigs (>= 0 bp)	3
 # contigs (>= 1000 bp)	3
 Total length (>= 0 bp)	6710
diff -r 0edbf19cf5eb -r 2f581f956e1c test-data/Quast_report.txt
--- a/test-data/Quast_report.txt	Wed Nov 02 09:42:45 2016 -0400
+++ b/test-data/Quast_report.txt	Fri Nov 04 05:06:15 2016 -0400
@@ -1,6 +1,6 @@
 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.fasta
+Assembly                   contigs_1_fasta
 # contigs (>= 0 bp)        3              
 # contigs (>= 1000 bp)     3              
 Total length (>= 0 bp)     6710