# HG changeset patch
# User elixir-it
# Date 1541761372 18000
# Node ID bf16e5399eb88642db0ab3b5771de63ecf3557db
Uploaded
diff -r 000000000000 -r bf16e5399eb8 bed_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_macros.xml Fri Nov 09 06:02:52 2018 -0500
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diff -r 000000000000 -r bf16e5399eb8 covacs_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_macros.xml Fri Nov 09 06:02:52 2018 -0500
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diff -r 000000000000 -r bf16e5399eb8 covacs_mpileup.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_mpileup.xml Fri Nov 09 06:02:52 2018 -0500
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+ samtools mpileup wrapper for covacs
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+ bed_macros.xml
+ covacs_macros.xml
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+ samtools
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+ $log
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+ ]]>
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+**more information** at http://www.htslib.org/doc/samtools-1.2.html
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+**Implemented options** samtools mpileup
+ -B, --no-BAQ disable BAQ (per-Base Alignment Quality)
+ -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]
+ -d, --max-depth INT max per-file depth; avoids excessive memory usage [8000]
+ -f, --fasta-ref FILE faidx indexed reference sequence file
+ -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)
+ -q, --min-MQ INT skip alignments with mapQ smaller than INT [0]
+ -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13]
+**fixed option**
+ -A, --count-orphans do not discard anomalous read pairs
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+ 10.1186/s12864-018-4508-1
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diff -r 000000000000 -r bf16e5399eb8 tool-data/covacs_bed.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/covacs_bed.loc.sample Fri Nov 09 06:02:52 2018 -0500
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+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory bed file for covacs sequences data files. You will need
+#to create these data files and then create a bed_loc.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bed_loc.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
+hg19 hg19 hg19-padded /export/BED/S07084713_Padded.bed
+hgbed hg19 hg19-bed-test /export/BED/chr22.bed
diff -r 000000000000 -r bf16e5399eb8 tool-data/covacs_gatk_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/covacs_gatk_indexes.loc.sample Fri Nov 09 06:02:52 2018 -0500
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+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of all covacs wrapper that need a gatk reference. You will need
+#to create these data files and then create a covacs_gatk_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The covacs_gatk_indexes.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.dict, phiX.fa.fai files.
+#
+#
+#Your covacs_gatk_indexes.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
+hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa
+hg19 hg19 hg19 /export/gatk_hg19_index_bundle/ucsc.hg19.fasta
diff -r 000000000000 -r bf16e5399eb8 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Nov 09 06:02:52 2018 -0500
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