Mercurial > repos > devteam > bwa
changeset 12:086ba7b646e5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
| author | iuc |
|---|---|
| date | Thu, 05 Sep 2019 19:35:56 -0400 |
| parents | 6def3ba376a7 |
| children | ceed4b724f0b |
| files | bwa-mem.xml bwa.xml read_group_macros.xml |
| diffstat | 3 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/bwa-mem.xml Tue Apr 10 18:40:10 2018 -0400 +++ b/bwa-mem.xml Thu Sep 05 19:35:56 2019 -0400 @@ -106,7 +106,7 @@ '${fastq_input.fastq_input1}' #end if -| samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output' +| samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output' ]]></command> <inputs>
--- a/bwa.xml Tue Apr 10 18:40:10 2018 -0400 +++ b/bwa.xml Thu Sep 05 19:35:56 2019 -0400 @@ -209,7 +209,7 @@ '${reference_fasta_filename}' first.sai '${input_type.bam_input}' #end if -| samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output' +| samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output' ]]> </command>
--- a/read_group_macros.xml Tue Apr 10 18:40:10 2018 -0400 +++ b/read_group_macros.xml Thu Sep 05 19:35:56 2019 -0400 @@ -242,7 +242,7 @@ <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> </xml> <xml name="read_group_pu_required_param"> - <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> + <param name="PU" type="text" value="run" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec">