Mercurial > repos > jdv > nanopolish
changeset 10:c00a942cfc0b draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 1eeffb2cd0b8115ca185f7fcb2df2920dff33e3b
| author | jdv |
|---|---|
| date | Mon, 12 Feb 2018 23:59:21 -0500 |
| parents | f1141f6a2d65 |
| children | 550ac6458c07 |
| files | nanopolish_variants.pl nanopolish_variants.xml test-data/consensus.empty.fa test-data/consensus.empty.vcf test-data/ref_empty.fa |
| diffstat | 2 files changed, 19 insertions(+), 5 deletions(-) [+] |
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--- 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;
--- 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> <!-- ***************************************************************** -->