Mercurial > repos > iuc > samtools_view
changeset 6:ff313de5f7f4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
| author | iuc |
|---|---|
| date | Thu, 17 Oct 2019 02:25:30 -0400 |
| parents | 90944a49ad05 |
| children | b01db2684fa5 |
| files | samtools_view.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/samtools_view.xml Mon Jul 29 08:50:15 2019 -0400 +++ b/samtools_view.xml Thu Oct 17 02:25:30 2019 -0400 @@ -120,14 +120,14 @@ ## then sort the output by coordinate, #if not $input.is_of_type('bam') and $outtype == 'bam': && samtools sort - -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp + -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -O bam -o 'tmpsam' outfile && mv tmpsam outfile #if $adv_output.outputpassing == 'yes': && samtools sort - -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp + -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -O bam -o 'tmpsam' inv_outfile @@ -228,7 +228,7 @@ <when value="cached"> <param name="ref" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> - <filter column="1" key="dbkey" ref="input" type="data_meta" /> + <filter column="dbkey" key="dbkey" ref="input" type="data_meta" /> <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> </options> </param>