# HG changeset patch
# User elixir-it
# Date 1541759259 18000
# Node ID c785cec34cdcfaabe379e94457acb3259ff79bd9
Uploaded
diff -r 000000000000 -r c785cec34cdc bed_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_macros.xml Fri Nov 09 05:27:39 2018 -0500
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diff -r 000000000000 -r c785cec34cdc covacs_ApplyRecalibrator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_ApplyRecalibrator.xml Fri Nov 09 05:27:39 2018 -0500
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+ gatk ApplyRecalibrator wrapper
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+ bed_macros.xml
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+ gatk
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+ $log
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+ ]]>
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+.. class:: warningmark
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+**IMPORTANT** to get the wrapper ready to start the admin user have to download gatk GATK version 3.8 from the broadinstitute site https://software.broadinstitute.org/gatk/download/archive and then move it in the conda_prefix folder, the path of the conda_prefix is written in the galaxy.ini(or .yml) file
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+ **more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_ApplyRecalibration.php
+
+-----
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+**implemented options** ApplyRecalibrator:
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+**-L** : One or more genomic intervals over which to operate(file.bed)
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+**-ip** : Amount of padding (in bp) to add to each interval
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+**-R** : Reference sequence file
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+**-ts\_filter_\level** : The truth sensitivity level at which to start filtering
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+**-tranchesFile** : Level of sensitivity. A tranchesfile is required. Please read the GATK manual if you do according to the input tranches file
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+**-recallFile** : The input recal file used by ApplyRecalibration
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+**-mode** : Recalibration mode to employ: SNP for recalibrating only SNPs, INDEL for indels
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+ 10.1186/s12864-018-4508-1
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diff -r 000000000000 -r c785cec34cdc mv_untar_gatk.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mv_untar_gatk.sh Fri Nov 09 05:27:39 2018 -0500
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+#!/bin/bash
+#if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm
+#and untar the archive
+if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then
+ tar -zxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.gz -C $CONDA_PREFIX/../../
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+else
+ echo GATK is present
+fi
diff -r 000000000000 -r c785cec34cdc 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 05:27:39 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 c785cec34cdc 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 05:27:39 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 c785cec34cdc 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 05:27:39 2018 -0500
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