Mercurial > repos > devteam > bwa
changeset 23:3fe632431b68 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 777181bd04849dab271ee2cc95e45c182947d308"
| author | iuc |
|---|---|
| date | Tue, 19 May 2020 11:29:11 -0400 |
| parents | 01ac0a5fedc3 |
| children | 64f11cf59c6e |
| files | bwa-mem.xml bwa.xml bwa_macros.xml |
| diffstat | 3 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/bwa-mem.xml Wed May 08 13:00:39 2019 -0400 +++ b/bwa-mem.xml Tue May 19 11:29:11 2020 -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 '$bam_output' ]]></command> <inputs>
--- a/bwa.xml Wed May 08 13:00:39 2019 -0400 +++ b/bwa.xml Tue May 19 11:29:11 2020 -0400 @@ -209,7 +209,7 @@ '${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/bwa_macros.xml Wed May 08 13:00:39 2019 -0400 +++ b/bwa_macros.xml Tue May 19 11:29:11 2020 -0400 @@ -114,8 +114,8 @@ **Specify read group information?** widget. If you are not familiar with read groups you shold know that this is effectively a way to tag reads with an additional ID. This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as instead of dealing with multiple datasets you only have to handle only one. This is possible because the read group information allows you to identify -data from different experiments even if they are combined in one file. Many downstream analysis tools such as varinat callers (e.g., FreeBayes or Naive Varinat Caller -present in Galaxy) are aware of readgtroups and will automatically generate calls for each individual sample even if they are combined within a single file. +data from different experiments even if they are combined in one file. Many downstream analysis tools such as variant callers (e.g., FreeBayes or Naive Variant Caller +present in Galaxy) are aware of read groups and will automatically generate calls for each individual sample even if they are combined within a single file. **Description of read groups fields**