# HG changeset patch # User iuc # Date 1725765786 0 # Node ID 4a1733940291ac86538480fe4820d09e83bbda2b # Parent 71db7f3a33b9e18d66d3d6b93155978d0bfebe01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c diff -r 71db7f3a33b9 -r 4a1733940291 macros.xml --- a/macros.xml Tue Sep 28 16:05:50 2021 +0000 +++ b/macros.xml Sun Sep 08 03:23:06 2024 +0000 @@ -5,8 +5,15 @@ - 1.13 - 20.05 + + 1.20 + 2 + 22.05 &2 && + gzip -dc \$reffa > reference.fa && + reffa="reference.fa" && + samtools faidx \$reffa; + } + } && + #end if + reffai=\$reffa.fai && #elif $addref_cond.addref_select == "cached": - #set reffa=str($addref_cond.ref.fields.path) - #set reffai=str($addref_cond.ref.fields.path)+".fai" + ## in case of cached the absolute path is used which allows to read + ## a cram file without specifying the reference + reffa='${addref_cond.ref.fields.path}' && + reffai=\$reffa.fai && #else - #set reffa=None - #set reffai=None + #set use_ref=False #end if ]]> - + @HELP@ @@ -179,37 +219,7 @@ - - @misc{SAM_def, - title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/},} - - 10.1093/bioinformatics/btp352 - 10.1093/bioinformatics/btr076 - 10.1093/bioinformatics/btr509 - - @misc{Danecek_et_al, - Author={Danecek, P., Schiffels, S., Durbin, R.}, - title={Multiallelic calling model in bcftools (-m)}, - url = {http://samtools.github.io/bcftools/call-m.pdf},} - - - @misc{Durbin_VCQC, - Author={Durbin, R.}, - title={Segregation based metric for variant call QC}, - url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} - - - @misc{Li_SamMath, - Author={Li, H.}, - title={Mathematical Notes on SAMtools Algorithms}, - url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} - - - @misc{SamTools_github, - title={SAMTools GitHub page}, - url = {https://github.com/samtools/samtools},} - + 10.1093/gigascience/giab008 diff -r 71db7f3a33b9 -r 4a1733940291 samtools_reheader.xml --- a/samtools_reheader.xml Tue Sep 28 16:05:50 2021 +0000 +++ b/samtools_reheader.xml Sun Sep 08 03:23:06 2024 +0000 @@ -1,4 +1,4 @@ - + copy SAM/BAM header between datasets macros.xml diff -r 71db7f3a33b9 -r 4a1733940291 test-data/reheader_out.bam Binary file test-data/reheader_out.bam has changed