Mercurial > repos > devteam > samtools_calmd
changeset 11:ff7764343c37 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
| author | iuc |
|---|---|
| date | Sun, 08 Sep 2024 03:22:05 +0000 |
| parents | dae754b6a98b |
| children | |
| files | macros.xml samtools_calmd.xml test-data/samtools_calmd_out_1.bam test-data/samtools_calmd_out_2.bam |
| diffstat | 4 files changed, 12 insertions(+), 35 deletions(-) [+] |
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--- a/macros.xml Sat Nov 27 12:28:24 2021 +0000 +++ b/macros.xml Sun Sep 08 03:22:05 2024 +0000 @@ -5,8 +5,15 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.13</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 @@ -103,7 +110,7 @@ #end if ]]></token> - <xml name="optional_reference"> + <xml name="optional_reference" token_help="" token_argument=""> <conditional name="addref_cond"> <param name="addref_select" type="select" label="Use a reference sequence"> <help>@HELP@</help> @@ -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_calmd.xml Sat Nov 27 12:28:24 2021 +0000 +++ b/samtools_calmd.xml Sun Sep 08 03:22:05 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_calmd" name="Samtools calmd" version="2.0.3" profile="@PROFILE@"> +<tool id="samtools_calmd" name="Samtools calmd" version="2.0.4" profile="@PROFILE@"> <description>recalculate MD/NM tags</description> <macros> <import>macros.xml</import>