Mercurial > repos > iuc > lofreq_call
comparison lofreq_call.xml @ 8:b11e8e9c23bf draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 814935de92514901b397ad335e9a43dba728973f
| author | iuc |
|---|---|
| date | Wed, 02 Oct 2024 08:20:25 +0000 |
| parents | 4805fe3d8fda |
| children |
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| 7:4805fe3d8fda | 8:b11e8e9c23bf |
|---|---|
| 1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2" profile="18.01"> | 1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy3" profile="18.01"> |
| 2 <description>with LoFreq</description> | 2 <description>with LoFreq</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 89 | 89 |
| 90 reads.bam 2>&1 | 90 reads.bam 2>&1 |
| 91 | 91 |
| 92 ## in case of errors add the log files produced | 92 ## in case of errors add the log files produced |
| 93 ## by the parallel workers to stderr | 93 ## by the parallel workers to stderr |
| 94 || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code) | 94 || (tool_exit_code=\$? && cat "\$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code) |
| 95 | 95 |
| 96 ## work around a bug in lofreq call-parallel | 96 ## work around a bug in lofreq call-parallel |
| 97 ## https://github.com/CSB5/lofreq/issues/85 | 97 ## https://github.com/CSB5/lofreq/issues/85 |
| 98 ## that causes the output format to be vcf.gz with certain filter | 98 ## that causes the output format to be vcf.gz with certain filter |
| 99 ## combinations. Issue is closed but still not fixed. | 99 ## combinations. Issue is closed but still not fixed. |