# HG changeset patch
# User elixir-it
# Date 1541759143 18000
# Node ID 03593410f057f91ad32d024f33e4e2c03569ca13
Uploaded
diff -r 000000000000 -r 03593410f057 bed_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_macros.xml Fri Nov 09 05:25:43 2018 -0500
@@ -0,0 +1,22 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 03593410f057 covacs_freebayes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_freebayes.xml Fri Nov 09 05:25:43 2018 -0500
@@ -0,0 +1,91 @@
+
+ Bayesian genetic variant detection, freebayes V = 1.2.0
+
+ covacs_macros.xml
+ bed_macros.xml
+
+
+ freebayes
+
+
+ $output
+
+
+ && perl $__tool_directory__/filter.fb.pl $output $output_filtered
+
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+**Currently available options**
+
+-f --fasta-reference FILE
+ Use FILE as the reference sequence for analysis.
+ An index file (FILE.fai) will be created if none exists.
+ If neither --targets nor --region are specified, FreeBayes
+ will analyze every position in this reference.
+
+-C --min-alternate-count N
+ Require at least this count of observations supporting
+ an alternate allele within a single individual in order
+ to evaluate the position.
+-t --targets FILE
+ Limit analysis to targets listed in the BED-format FILE.
+
+**Two output file are generated**
+
+The first output consists in a vcf file containing all the variants detected by Freebayes, the second file contains a subset of the variants filtered according to their QUAL score (QUAL >=20), see the CoVaCS paper for more details.
+
+
+
+
+ 10.1186/s12864-018-4508-1
+
+ @misc{1207.3907,
+ Author = {Erik Garrison},
+ Title = {Haplotype-based variant detection from short-read sequencing},
+ Year = {2012},
+ Eprint = {arXiv:1207.3907},
+ url = {http://arxiv.org/abs/1207.3907}
+ }
+
+
+
+
diff -r 000000000000 -r 03593410f057 covacs_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_macros.xml Fri Nov 09 05:25:43 2018 -0500
@@ -0,0 +1,22 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 03593410f057 filter.fb.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.fb.pl Fri Nov 09 05:25:43 2018 -0500
@@ -0,0 +1,21 @@
+#!/usr/bin/perl -w
+#
+$f=shift;
+$out=shift;
+open(IN,$f);
+open(OUT,">$out");
+while()
+{
+ if ($_=~/^#/)
+ {
+ print OUT;
+ next;
+ }else{
+ $vl=(split())[5];
+ $gt=(split())[-1];
+ $gt=(split(/\:/,$gt))[0];
+ next if $gt eq "0/0";
+ print OUT if $vl>20;
+ }
+}
+close(OUT);
diff -r 000000000000 -r 03593410f057 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 05:25:43 2018 -0500
@@ -0,0 +1,17 @@
+#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 03593410f057 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 05:25:43 2018 -0500
@@ -0,0 +1,36 @@
+#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 03593410f057 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 05:25:43 2018 -0500
@@ -0,0 +1,12 @@
+
+
+