Mercurial > repos > devteam > samtools_split
changeset 7:b6caca6a4ca5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
| author | iuc |
|---|---|
| date | Sun, 08 Sep 2024 03:23:35 +0000 |
| parents | eda9f7aa1d54 |
| children | |
| files | macros.xml samtools_split.xml test-data/phiX_Elephant.bam test-data/phiX_Human.bam test-data/phiX_Mouse.bam test-data/samtools_split_out.bam |
| diffstat | 6 files changed, 15 insertions(+), 39 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Mon Aug 15 09:12:10 2022 +0000 +++ b/macros.xml Sun Sep 08 03:23:35 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_split.xml Mon Aug 15 09:12:10 2022 +0000 +++ b/samtools_split.xml Sun Sep 08 03:23:35 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>BAM dataset on readgroups</description> <macros> <import>macros.xml</import> @@ -8,12 +8,11 @@ <expand macro="version_command"/> <command><![CDATA[ @ADDTHREADS@ - samtools split -f 'Read_Group_%!.bam' + samtools split -f 'Read_Group_%!.bam' --output-fmt 'bam' #if $header: - -u '${output}:${header}' - #else: - -u '${output}' + -h $header' #end if + -u '$output' -@ \$addthreads '$input_bam' ]]></command> @@ -41,7 +40,7 @@ Splits BAM files on readgroups. -This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. +This tool is based on ``samtools split`` command. It will generate multiple output datasets for each readgroup from the input dataset. ]]></help> <expand macro="citations"/> </tool>