Mercurial > repos > iuc > samtools_ampliconclip
changeset 2:b5f87b4cfda6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
| author | iuc |
|---|---|
| date | Sun, 08 Sep 2024 03:21:59 +0000 |
| parents | d90472d5f10a |
| children | |
| files | macros.xml samtools_ampliconclip.xml test-data/eboVir3.clipped.bam test-data/eboVir3.clipped.strand.bam test-data/eboVir3.clipped.strand_gt30.bam test-data/eboVir3.hardclipped.bam |
| diffstat | 6 files changed, 15 insertions(+), 38 deletions(-) [+] |
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--- a/macros.xml Mon Aug 15 09:07:14 2022 +0000 +++ b/macros.xml Sun Sep 08 03:21:59 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_ampliconclip.xml Mon Aug 15 09:07:14 2022 +0000 +++ b/samtools_ampliconclip.xml Sun Sep 08 03:21:59 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>clip primer bases from bam files</description> <macros> <import>macros.xml</import> @@ -29,11 +29,11 @@ <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" /> <param name="input_bam" type="data" format="bam" label="BAM file" /> <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" /> - <param name="strand" argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" /> - <param name="both_ends" argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" /> - <param name="no_excluded" argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" /> + <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" /> + <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" /> + <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" /> <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" /> - <param name="tolerance" argument="--tolerance" type="integer" value="5" min="0" label="Tolerance" help="match region within this number of bases, default 5." /> + <param argument="--tolerance" type="integer" value="5" min="0" label="Tolerance" help="match region within this number of bases, default 5." /> </inputs> <outputs>