Mercurial > repos > lparsons > htseq_count
changeset 29:44c91703f6a5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 9b894593cf3c0156faf679300ded731e0796f792"
| author | iuc |
|---|---|
| date | Mon, 27 Jan 2020 04:42:43 +0000 |
| parents | bc4ada69b61f |
| children | d29e87f5a250 |
| files | htseq-count.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/htseq-count.xml Thu Oct 10 04:05:45 2019 -0400 +++ b/htseq-count.xml Mon Jan 27 04:42:43 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="htseq_count" name="htseq-count" version="0.9.1" profile="16.04"> +<tool id="htseq_count" name="htseq-count" version="0.9.1+galaxy1" profile="16.04"> <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> <requirements> <requirement type="package" version="0.9.1">htseq</requirement> @@ -49,7 +49,7 @@ --secondary-alignments=${advanced_options.secondary_alignments} --supplementary-alignments=${advanced_options.supplementary_alignments} #if $advanced_options.samout_conditional.samout == "Yes": - --samout='$__new_file_path__/${samoutfile.id}_tmp.sam' + --samout=samout.sam #end if #end if @@ -65,7 +65,7 @@ #if $advanced_options.samout_conditional.samout == "Yes": && samtools view -Su -t '${reference_fasta_filename}.fai' - '$__new_file_path__/${samoutfile.id}_tmp.sam' + samout.sam | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' - #end if #end if