Mercurial > repos > iuc > samtools_merge
changeset 5:84f122ab14d6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
| author | iuc |
|---|---|
| date | Sun, 08 Sep 2024 03:23:00 +0000 |
| parents | 95fd8bf80632 |
| children | |
| files | macros.xml samtools_merge.xml test-data/1.merge.expected.bam test-data/2.merge.expected.bam test-data/3.merge.expected.bam test-data/4.merge.expected.bam test-data/5.merge.expected.bam test-data/6.merge.expected.bam |
| diffstat | 8 files changed, 14 insertions(+), 37 deletions(-) [+] |
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--- a/macros.xml Mon Aug 15 09:11:35 2022 +0000 +++ b/macros.xml Sun Sep 08 03:23:00 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_merge.xml Mon Aug 15 09:11:35 2022 +0000 +++ b/samtools_merge.xml Sun Sep 08 03:23:00 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>merge multiple sorted alignment files</description> <macros> <import>macros.xml</import> @@ -38,7 +38,7 @@ samtools merge -@ \$addthreads -s $seed -## TODO force overwrite seems necessay (but I do not understand why ...) +## force overwrite seems necessay (but I do not understand why ...) -f ## Galaxy provides only default compression ## #if $compression == 'levelone' @@ -52,14 +52,14 @@ #if $sortby=='name' -n #end if -## TODO since galaxy can't represent this as data type at the moment this option is unsupported +## since galaxy can't represent this as data type at the moment this option is unsupported ## -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given). #if str($region) != '' -R '$region' #end if ## Attach an RG tag to each alignment. The tag value is inferred from file names. ## -r -## TODO -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used? +## -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used? #if $bed_file: -L '$bed_file' #end if