Mercurial > repos > iuc > lofreq_call
changeset 6:e1461b5c52a0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit c1fda24943cf04866d408133ffb6aabf4a90866b"
| author | iuc |
|---|---|
| date | Mon, 05 Oct 2020 20:14:06 +0000 |
| parents | 65432c3abf6c |
| children | 4805fe3d8fda |
| files | lofreq_call.xml |
| diffstat | 1 files changed, 3 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/lofreq_call.xml Mon Jun 15 13:13:03 2020 -0400 +++ b/lofreq_call.xml Mon Oct 05 20:14:06 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy0"> +<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1" profile="18.01"> <description>with LoFreq</description> <macros> <import>macros.xml</import> @@ -34,11 +34,6 @@ ## call variants with lofreq - ## make lofreq stick to tool contract by - ## generating tmp output inside job working dir - mkdir pp-tmp && - export TMPDIR=pp-tmp && - lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose --ref '$reference_fasta_fn' --out variants.vcf $variant_types @@ -96,12 +91,12 @@ ## in case of errors add the log files produced ## by the parallel workers to stderr - || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code) + || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code) ## work around a bug in lofreq call-parallel ## https://github.com/CSB5/lofreq/issues/85 ## that causes the output format to be vcf.gz with certain filter - ## combinations. + ## combinations. Issue is closed but still not fixed. #if str($bonf_factor) != 'dynamic': #if '--no-default-filter' in str($filter_control.others): && ln -s variants.vcf variants.vcf.gz