# HG changeset patch
# User iuc
# Date 1700518542 0
# Node ID fa5d3e61e42974419ee51902fec75cbc0a441b4b
# Parent 7def34e6cf4de1f8f3216b1925ce7d7c637052df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit cd62639660bef041ba14ecff337fb98e84e75d8a
diff -r 7def34e6cf4d -r fa5d3e61e429 macros.xml
--- a/macros.xml Tue Sep 28 16:14:00 2021 +0000
+++ b/macros.xml Mon Nov 20 22:15:42 2023 +0000
@@ -5,7 +5,14 @@
- 1.13
+
+ 1.15.1
+ 2
20.05
&2 &&
+ gzip -dc \$reffa > reference.fa &&
+ reffa="reference.fa" &&
+ samtools faidx \$reffa;
+ }
+ } &&
+ #end if
+ reffai=\$reffa.fai &&
#elif $addref_cond.addref_select == "cached":
- #set reffa=str($addref_cond.ref.fields.path)
- #set reffai=str($addref_cond.ref.fields.path)+".fai"
+ ## in case of cached the absolute path is used which allows to read
+ ## a cram file without specifying the reference
+ reffa='${addref_cond.ref.fields.path}' &&
+ reffai=\$reffa.fai &&
#else
- #set reffa=None
- #set reffai=None
+ #set use_ref=False
#end if
]]>
-
+
@HELP@
@@ -179,37 +219,7 @@
-
- @misc{SAM_def,
- title={Definition of SAM/BAM format},
- url = {https://samtools.github.io/hts-specs/},}
-
- 10.1093/bioinformatics/btp352
- 10.1093/bioinformatics/btr076
- 10.1093/bioinformatics/btr509
-
- @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},}
-
-
- @misc{Durbin_VCQC,
- Author={Durbin, R.},
- title={Segregation based metric for variant call QC},
- url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-
-
- @misc{Li_SamMath,
- Author={Li, H.},
- title={Mathematical Notes on SAMtools Algorithms},
- url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-
-
- @misc{SamTools_github,
- title={SAMTools GitHub page},
- url = {https://github.com/samtools/samtools},}
-
+ 10.1093/gigascience/giab008
diff -r 7def34e6cf4d -r fa5d3e61e429 samtools_idxstats.xml
--- a/samtools_idxstats.xml Tue Sep 28 16:14:00 2021 +0000
+++ b/samtools_idxstats.xml Mon Nov 20 22:15:42 2023 +0000
@@ -1,4 +1,4 @@
-
+
reports stats of the BAM index file
macros.xml