# HG changeset patch
# User iuc
# Date 1656360479 0
# Node ID a941babb926863e6f4b33eb4e7c2034976d5d824
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
diff -r 000000000000 -r a941babb9268 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Jun 27 20:07:59 2022 +0000
@@ -0,0 +1,256 @@
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+ samtools
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+ 1.13
+ 20.05
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+
+
+ &2 &&
+ gzip -dc \$reffa > reference.fa &&
+ reffa="reference.fa" &&
+ samtools faidx \$reffa;
+ }
+ } &&
+ #end if
+ reffai=\$reffa.fai &&
+ #elif $addref_cond.addref_select == "cached":
+ ## in case of cached the absolute path is used which allows to read
+ ## a cram file without specifying the reference
+ reffa='${addref_cond.ref.fields.path}' &&
+ reffai=\$reffa.fai &&
+ #else
+ #set use_ref=False
+ #end if
+ ]]>
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+ @HELP@
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+ @HELP@
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+ ^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$
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+ @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},}
+
+
+
+
+ &1 | grep Version]]>
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diff -r 000000000000 -r a941babb9268 samtools_ampliconclip.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_ampliconclip.xml Mon Jun 27 20:07:59 2022 +0000
@@ -0,0 +1,83 @@
+
+ clip primer bases from bam files
+
+ macros.xml
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+**What it does**
+ Clips read alignments where they match BED file defined regions (e.g. for amplicon sequencing).
+
+ samtools ampliconclip -b [INPUT BED] [INPUT BAM1] -o [OUTPUT]
+
+
+
diff -r 000000000000 -r a941babb9268 test-data/eboVir3.1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eboVir3.1.bed Mon Jun 27 20:07:59 2022 +0000
@@ -0,0 +1,3 @@
+eboVir3 500 1500 1 0 -
+eboVir3 1500 2000 2 0 +
+eboVir3 1500 3000 3 0 -
diff -r 000000000000 -r a941babb9268 test-data/eboVir3.bam
Binary file test-data/eboVir3.bam has changed
diff -r 000000000000 -r a941babb9268 test-data/eboVir3.clipped.bam
Binary file test-data/eboVir3.clipped.bam has changed
diff -r 000000000000 -r a941babb9268 test-data/eboVir3.clipped.strand.bam
Binary file test-data/eboVir3.clipped.strand.bam has changed
diff -r 000000000000 -r a941babb9268 test-data/eboVir3.clipped.strand_gt30.bam
Binary file test-data/eboVir3.clipped.strand_gt30.bam has changed
diff -r 000000000000 -r a941babb9268 test-data/eboVir3.hardclipped.bam
Binary file test-data/eboVir3.hardclipped.bam has changed
diff -r 000000000000 -r a941babb9268 test-data/rebuild_output_bams.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rebuild_output_bams.sh Mon Jun 27 20:07:59 2022 +0000
@@ -0,0 +1,4 @@
+samtools ampliconclip -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.bam
+samtools ampliconclip --strand -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.strand.bam
+samtools ampliconclip --hard-clip -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.hardclipped.bam
+samtools ampliconclip --both-ends --no-excluded --strand --fail-len 30 -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.strand_gt30.bam