Mercurial > repos > iuc > samtools_bam_to_cram
changeset 7:b5386f2f01e7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
| author | iuc |
|---|---|
| date | Sun, 08 Sep 2024 03:21:31 +0000 |
| parents | 6c790feb4215 |
| children | |
| files | macros.xml samtools_bam_to_cram.xml test-data/test2.cram test-data/test_bam.cram test-data/test_chr1.cram test-data/test_regions.cram test-data/test_sam.cram |
| diffstat | 7 files changed, 11 insertions(+), 34 deletions(-) [+] |
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--- a/macros.xml Mon Aug 15 09:06:00 2022 +0000 +++ b/macros.xml Sun Sep 08 03:21:31 2024 +0000 @@ -5,8 +5,15 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.15.1</token> - <token name="@PROFILE@">20.05</token> + <!-- NOTE: for some tools only the version of the requirement but not the + tool's version is controlled by the TOOL_VERSION token + (because their version is ahead of the requirement version .. + please only bump the minor version in order to let the requirement + version catch up eventually). To find the tools check: + `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` --> + <token name="@TOOL_VERSION@">1.20</token> + <token name="@VERSION_SUFFIX@">2</token> + <token name="@PROFILE@">22.05</token> <token name="@FLAGS@"><![CDATA[ #set $flags = 0 #if $filter @@ -212,37 +219,7 @@ <xml name="citations"> <citations> - <citation type="bibtex"> - @misc{SAM_def, - title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/},} - </citation> - <citation type="doi">10.1093/bioinformatics/btp352</citation> - <citation type="doi">10.1093/bioinformatics/btr076</citation> - <citation type="doi">10.1093/bioinformatics/btr509</citation> - <citation type="bibtex"> - @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},} - </citation> - <citation type="bibtex"> - @misc{Durbin_VCQC, - Author={Durbin, R.}, - title={Segregation based metric for variant call QC}, - url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} - </citation> - <citation type="bibtex"> - @misc{Li_SamMath, - Author={Li, H.}, - title={Mathematical Notes on SAMtools Algorithms}, - url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} - </citation> - <citation type="bibtex"> - @misc{SamTools_github, - title={SAMTools GitHub page}, - url = {https://github.com/samtools/samtools},} - </citation> + <citation type="doi">10.1093/gigascience/giab008</citation> </citations> </xml> <xml name="version_command">
--- a/samtools_bam_to_cram.xml Mon Aug 15 09:06:00 2022 +0000 +++ b/samtools_bam_to_cram.xml Sun Sep 08 03:21:31 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>convert BAM alignments to CRAM format</description> <macros>