diff quast.xml @ 3:6fcbee531de6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67

--- a/quast.xml	Fri Nov 04 05:06:15 2016 -0400
+++ b/quast.xml	Fri Sep 29 05:51:26 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="quast" name="Quast" version="4.1.1" >
+<tool id="quast" name="Quast" version="4.5" >
     <description>Genome assembly Quality</description>
     <requirements>
-        <requirement type="package" version="4.1">quast</requirement>
+        <requirement type="package" version="4.5">quast</requirement>
     </requirements>
     <stdio>
         <regex match="ERROR! exception caught!"
@@ -13,6 +13,7 @@
     <![CDATA[
         #import re
         quast
+        --threads \${GALAXY_SLOTS:-4}
         -o outputdir
         #if $gene_selection == "eukaryote":
             --eukaryote
@@ -34,7 +35,7 @@
         --min-contig $min_contig
         -l
         #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ])
-        
+
         $names
         --contig-thresholds $threshold_contig
         #for $k in $files:
@@ -48,7 +49,7 @@
         mv outputdir/report.tsv '$quast_tsv' &&
         mv outputdir/report.tex '$quast_tex' &&
         mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' &&
-        mv outputdir/report.html '$report_html' 
+        mv outputdir/report.html '$report_html'
     ]]>
     </command>
     <inputs>
@@ -91,6 +92,21 @@
             <param name="gene_selection" value="prokaryotes"/>
             <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/>
         </test>
+        <test>
+            <param name="input" value="contigs_1.fasta"/>
+            <param name="input.type_file" value="contig"/>
+            <param name="input_ref" value="NC000913.3_1-6650.fasta"/>
+            <param name="gene_selection" value="prokaryotes"/>
+            <output name="quast_tsv" file="Quast_report_withref.tsv" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="input" value="contigs_1.fasta"/>
+            <param name="input.type_file" value="contig"/>
+            <param name="input_ref" value="NC000913.3_1-6650.fasta"/>
+            <param name="annot" value="NC000913.3_1-6650.gff"/>
+            <param name="gene_selection" value="prokaryotes"/>
+            <output name="quast_tsv" file="Quast_report_withref_withgenes.tsv" lines_diff="4"/>
+        </test>
     </tests>
     <help>
 <![CDATA[