# HG changeset patch
# User jdv
# Date 1518497961 18000
# Node ID c00a942cfc0be78bcd82844d667ded2070ca390f
# Parent  f1141f6a2d6576e103310f438a30e9c0a62fc314
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 1eeffb2cd0b8115ca185f7fcb2df2920dff33e3b

diff -r f1141f6a2d65 -r c00a942cfc0b nanopolish_variants.pl
--- a/nanopolish_variants.pl	Mon Feb 12 23:15:26 2018 -0500
+++ b/nanopolish_variants.pl	Mon Feb 12 23:59:21 2018 -0500
@@ -98,11 +98,13 @@
 my @regions :shared;
 
 # build region tags to pass to nanopolish
-my $parser = BioX::Seq::Stream->new($fn_genome);
-while (my $seq = $parser->next_seq) {
-    push @regions, join( ':', $seq->id,
-        join( '-', 1, length($seq) ),
-    );
+if (-s $fn_genome) { # gracefully handle empty inputs
+    my $parser = BioX::Seq::Stream->new($fn_genome);
+    while (my $seq = $parser->next_seq) {
+        push @regions, join( ':', $seq->id,
+            join( '-', 1, length($seq) ),
+        );
+    }
 }
 
 my @workers;
diff -r f1141f6a2d65 -r c00a942cfc0b nanopolish_variants.xml
--- a/nanopolish_variants.xml	Mon Feb 12 23:15:26 2018 -0500
+++ b/nanopolish_variants.xml	Mon Feb 12 23:59:21 2018 -0500
@@ -136,6 +136,18 @@
                 <has_text text="--calculate-all-support" />
             </assert_command>
         </test>
+        <!-- test empty input (should return empty output, not throw error) -->
+        <!-- currently empty inputs don't work, so this test is disabled
+        <test>
+            <param name="input_reads" value="called.fa" ftype="fasta" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="input_bam"   value="called.bam" ftype="bam" />
+            <param name="input_ref"   value="ref_empty.fa" ftype="fasta" />
+            <param name="input_index" value="index.tar" ftype="tar" />
+            <output name="out_consensus" file="consensus.empty.fa" compare="diff" />
+            <output name="out_variants" file="consensus.empty.vcf" compare="diff" />
+        </test>
+        -->
     </tests>
 
     <!-- ***************************************************************** -->
diff -r f1141f6a2d65 -r c00a942cfc0b test-data/consensus.empty.fa
diff -r f1141f6a2d65 -r c00a942cfc0b test-data/consensus.empty.vcf
diff -r f1141f6a2d65 -r c00a942cfc0b test-data/ref_empty.fa