Mercurial > repos > lparsons > htseq_count
diff htseq-count.xml @ 27:67b0b160903a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
| author | iuc |
|---|---|
| date | Thu, 17 Oct 2019 03:01:55 -0400 |
| parents | 7f5a8d427b39 |
| children | 916cb26bd9d3 |
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--- a/htseq-count.xml Sun Apr 29 09:53:13 2018 -0400 +++ b/htseq-count.xml Thu Oct 17 03:01:55 2019 -0400 @@ -32,9 +32,9 @@ #end if #if $samfile.extension == 'bam': - samtools sort -n --output-fmt=SAM -o '$name_sorted_alignment_filename' '$samfile' && + samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' '$samfile' && #else - samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n --output-fmt=SAM -o '$name_sorted_alignment_filename' - && + samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' - && #end if htseq-count @@ -66,7 +66,7 @@ && samtools view -Su -t '${reference_fasta_filename}.fai' '$__new_file_path__/${samoutfile.id}_tmp.sam' - | samtools sort -o '$samoutfile' - + | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' - #end if #end if ]]> @@ -128,7 +128,7 @@ <when value="cached"> <param name="ref_file" type="select" label="Using reference genome"> <options from_data_table="sam_fa_indexes"> - <filter type="data_meta" key="dbkey" ref="samfile" column="1"/> + <filter type="data_meta" key="dbkey" ref="samfile" column="value"/> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param>