# HG changeset patch
# User yhoogstrate
# Date 1446735423 18000
# Node ID 23e5913327b44c540dfc9f83be30e5b96532dde3
# Parent d2424abb94046c1a6787a47769ea64f5673abff5
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
diff -r d2424abb9404 -r 23e5913327b4 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,102 @@
+VarScan2 mpileup2snp wrapper for Galaxy
+=======================================
+
+http://sourceforge.net/projects/varscan/
+
+This wrapper is optimized for direct access to BAM files such that the
+big mpileup files are not saved.
+
+Development
+-----------
+
+Repository-Maintainer: Youri Hoogstrate
+
+Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
+
+
+License
+-------
+
+**VarScan2**:
+
+Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0): http://sourceforge.net/directory/os:linux/license:nposl3/freshness:recently-updated/ http://opensource.org/licenses/NPOSL-3.0
+
+**samtools**:
+
+MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE
+
+ The MIT/Expat License
+
+ Copyright (C) 2008-2014 Genome Research Ltd.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
+ [The use of a range of years within a copyright notice in this distribution
+ should be interpreted as being equivalent to a list of years including the
+ first and last year specified and all consecutive years between them.
+
+ For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
+ 2011-2012" should be interpreted as being identical to a notice that reads
+ "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
+ that reads "Copyright (C) 2005-2012" should be interpreted as being identical
+ to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
+ 2011, 2012".]
+
+**samtools-parallel-mpileup**:
+
+MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING
+
+The MIT License
+
+ Copyright (c) 2008-2009 Genome Research Ltd.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+**This wrapper**:
+
+ Copyright (C) 2013-2014 Youri Hoogstrate
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
diff -r d2424abb9404 -r 23e5913327b4 example.fa.1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example.fa.1.bed Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,1 @@
+chr1 0 330
diff -r d2424abb9404 -r 23e5913327b4 example.fa.2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example.fa.2.bed Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,1 @@
+chr1 330 600
diff -r d2424abb9404 -r 23e5913327b4 samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml Wed Nov 19 10:04:52 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,261 +0,0 @@
-
-
- Samtools mpileup (supporting parallelization)
-
- ncurses
- samtools_parallel_mpileup_0_1_19a
- package_samtools_0_1_19
-
-
- #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
- echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
- #else
- #if $mpileup_parallelization.mpileup_parallelization_select == "true"
- samtools-parallel-mpileup mpileup
- -t $mpileup_parallelization.samtools_threads
- #else
- samtools mpileup
- #end if
- -f
- #if $reference_genome_source.source_select == "indexed_filtered"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "indexed_all"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "history"
- "$reference_genome_source.reference_genome"
- #else
-
- "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
- #end if
-
- #if $extended_parameters_regions.samtools_regions == "region"
- -r $extended_parameters_regions.$samtools_r
- #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
- -l $extended_parameters_regions.$samtools_l
- #end if
-
- #if $extended_parameters.parameters == "extended"
- $extended_parameters.samtools_6
- $extended_parameters.samtools_A
- $extended_parameters.samtools_B
- -C $extended_parameters.samtools_C
- -d $extended_parameters.samtools_d
- $extended_parameters.samtools_E
- -M $extended_parameters.samtools_M
- $extended_parameters.samtools_R
- -q $extended_parameters.samtools_q
- -Q $extended_parameters.samtools_Q
-
- -e $extended_parameters.samtools_e
- -F $extended_parameters.samtools_F
- -h $extended_parameters.samtools_h
- $extended_parameters.samtools_I
- -L $extended_parameters.samtools_L
- -m $extended_parameters.samtools_m
- -o $extended_parameters.samtools_o
- $extended_parameters.samtools_p
- -P $extended_parameters.samtools_P
- #end if
-
- #for $alignment in $alignments
- ${alignment}
- #end for
-
- 2> stderr_1.txt
-
- #if $sort_mpileup
- | sort -k 1,1 -k 2,2
- #end if
-
- > $output ;
- cat stderr_1.txt
- #end if
-
-
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-
-
-**Samtools mpileup (supporting parallelization)**
-
-SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:
-
-Is flexible enough to store all the alignment information generated by various alignment programs;
-Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
-Is compact in file size;
-Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
-Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.
-SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-
-SAMtools is hosted by SourceForge.net. The project page is http://samtools.sourceforge.net/. The source code releases are available from the download page. You can check out the most recent source code from the github project page with:
-git clone git://github.com/samtools/samtools.git
-https://github.com/mydatascience/parallel-mpileup/
-
-Because samtools does not support parallization of the mpileup command, the project was forked to include paralellization support:
-
-
-However, since the project seems to lack support and contains fatal bugs this project was continued at:
-https://github.com/yhoogstrate/parallel-mpileup/
-
-
-**Input formats**
-
-Satmools accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing.
-
-**Installation**
-
-The installation is fully automatic.
-
-**License**
-
-* parallel-mpileup: MIT License (https://github.com/yhoogstrate/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
-* samtool: MIT License
-
-
-**Contact**
-
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
-http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
-
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-http://toolshed.dtls.nl/
-
-
\ No newline at end of file
diff -r d2424abb9404 -r 23e5913327b4 test-data/GSM1244822_Control_Rep7.hg18.subset.chr10_8136673-8157170.bam
Binary file test-data/GSM1244822_Control_Rep7.hg18.subset.chr10_8136673-8157170.bam has changed
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.bam
Binary file test-data/example.bam has changed
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,11 @@
+>chr1
+aaataggtcccaaacgttacgcactctatgcctgacaaagttgcgaccacttcctctgcc
+ttgtgtgacacgccggagatagggcatcagcaagtacgttaagtacactgaacgaactgg
+aggtttctacatcgtgcgtgatggctctaggagaagtgggtgtatctgcacagcataagt
+tataagacggaagtaaagcgtcttcaccgttcagcaccccacgctcatagtcaatgctgg
+ttcagcatagtcaagcgccggtggcctccaaaaagacgcactgagtagcttagctacttt
+gctccgcttgcggaagcactaagaggagattgaatttccaaatcccccccgatacctgtg
+cggtcgctacgtaagtgcgaagttctgttagatacgctccccttagtatatgggcgttaa
+tcggaccgtcggtactcactgcattccaggtctcatatagttcgccctagaagcctggga
+tgaacgttgaactatagctgatgtaaaccccgcgtgccaattccaggcgtcatgggggca
+acccctcgcagcctccctcttgctgttggtgcctagtatttcatgatttcgagccgacat
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.fa.1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa.1.bed Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,1 @@
+chr1 0 330
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.fa.2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa.2.bed Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,1 @@
+chr1 330 600
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa.fai Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,1 @@
+chr1 600 6 60 61
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.mpileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.mpileup Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,70 @@
+chr1 1 a 8 ^],^].^],^].^],^],^].^], ~~~~~~~~
+chr1 2 a 8 ,.,.,,., ~~~~~~~~
+chr1 3 a 8 ,.,.,,., ~~~~~~~~
+chr1 4 t 8 ,.,.,,., ~~~~~~~~
+chr1 5 a 8 ,.,.,,., ~~~~~~~~
+chr1 6 g 8 ,.,.,,., ~~~~~~~~
+chr1 7 g 8 ,.,.,,., ~~~~~~~~
+chr1 8 t 8 ,.,.,,., ~~~~~~~~
+chr1 9 c 8 ,.,.,,., ~~~~~~~~
+chr1 10 c 8 ,.,.,,., ~~~~~~~~
+chr1 11 c 8 ,.,.,,., ~~~~~~~~
+chr1 12 a 8 ,.,.,,., ~~~~~~~~
+chr1 13 a 8 ,.,.,,., ~~~~~~~~
+chr1 14 a 8 ,.,.,,., ~~~~~~~~
+chr1 15 c 8 ,.,.,,., ~~~~~~~~
+chr1 16 g 8 ,.,.,,., ~~~~~~~~
+chr1 17 t 8 ,-1t.-1T,-1t.-1T,-1t,-1t.-1T,-1t ~~~~~~~~
+chr1 18 t 8 ******** ~~~~~~~~
+chr1 19 a 8 ,.,.,,., ~~~~~~~~
+chr1 20 c 8 ,.,.,,., ~~~~~~~~
+chr1 21 g 8 ,.,.,,., ~~~~~~~~
+chr1 22 c 8 ,.,.,,., ~~~~~~~~
+chr1 23 a 8 ,.,.,,., ~~~~~~~~
+chr1 24 c 8 gGgGggGg ~~~~~~~~
+chr1 25 t 8 ,.,.,,., ~~~~~~~~
+chr1 26 c 8 ,.,.,,., ~~~~~~~~
+chr1 27 t 8 ,.,.,,., ~~~~~~~~
+chr1 28 a 8 ,.,.,,., ~~~~~~~~
+chr1 29 t 8 ,.,.,,., ~~~~~~~~
+chr1 30 g 8 ,.,.,,., ~~~~~~~~
+chr1 31 c 8 ,.,.,,., ~~~~~~~~
+chr1 32 c 8 ,.,.,,., ~~~~~~~~
+chr1 33 t 8 ,.,.,,., ~~~~~~~~
+chr1 34 g 8 ,.,.,,., ~~~~~~~~
+chr1 35 a 8 ,$.$,$.$,$,$.$,$ ~~~~~~~~
+chr1 61 t 8 ^],^],^],^],^],^],^],^], ~BBBBBBB
+chr1 62 t 8 ,,,,,,,, ~EEEEEEE
+chr1 63 g 8 ,,,,,,,, ~bbbbbbb
+chr1 64 t 8 ,,,,,,,, ~eeeeeee
+chr1 65 g 8 ,,,,,,,, ~ooooooo
+chr1 66 t 8 ,,,,,,,, ~ppppppp
+chr1 67 g 8 ,,,,,,,, ~sssssss
+chr1 68 a 8 ,,,,,,,, ~xxxxxxx
+chr1 69 c 8 ,,,,,,,, ~xxxxxxx
+chr1 70 a 8 ,,,,,,,, ~xxxxxxx
+chr1 71 c 8 ,,,,,,,, ~xxxxxxx
+chr1 72 g 8 ,,,,,,,, ~{{{{{{{
+chr1 73 c 8 ,,,,,,,, ~aaaaaaa
+chr1 74 c 8 ,,,,,,,, ~aaaaaaa
+chr1 75 g 8 ,,,,,,,, ~RRRRRRR
+chr1 76 g 8 ,,,,,,,, ~RRRRRRR
+chr1 77 a 1 ,+1a ~
+chr1 78 g 8 ,,,,,,,, ~RRRRRRR
+chr1 79 a 8 ,,,,,,,, ~RRRRRRR
+chr1 80 t 8 ,,,,,,,, ~[[[[[[[
+chr1 81 a 8 ,,,,,,,, ~[[[[[[[
+chr1 82 g 8 ,,,,,,,, ~[[[[[[[
+chr1 83 g 8 ,,,,,,,, ~[[[[[[[
+chr1 84 g 8 aaaaaaaa ~[[[[[[[
+chr1 85 c 8 ,,,,,,,, ~[[[[[[[
+chr1 86 a 8 ,,,,,,,, ~[[[[[[[
+chr1 87 t 8 ,,,,,,,, ~iiiiiii
+chr1 88 c 8 ,,,,,,,, ~iiiiiii
+chr1 89 a 8 ,,,,,,,, ~lllllll
+chr1 90 g 8 ,,,,,,,, ~~~~~~~~
+chr1 91 c 8 ,,,,,,,, ~~~~~~~~
+chr1 92 a 8 ,,,,,,,, ~aaaaaaa
+chr1 93 a 8 ,,,,,,,, ~_______
+chr1 94 g 8 ,,,,,,,, ~UUUUUUU
+chr1 95 t 8 ,$,$,$,$,$,$,$,$ ~EEEEEEE
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.mpileup.parallel
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.mpileup.parallel Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,70 @@
+achr1 77 a 1 ,+1a ~
+chr1 1 a 8 ^],^].^],^].^],^],^].^], ~~~~~~~~
+chr1 2 a 8 ,.,.,,., ~~~~~~~~
+chr1 3 a 8 ,.,.,,., ~~~~~~~~
+chr1 4 t 8 ,.,.,,., ~~~~~~~~
+chr1 5 a 8 ,.,.,,., ~~~~~~~~
+chr1 6 g 8 ,.,.,,., ~~~~~~~~
+chr1 7 g 8 ,.,.,,., ~~~~~~~~
+chr1 8 t 8 ,.,.,,., ~~~~~~~~
+chr1 9 c 8 ,.,.,,., ~~~~~~~~
+chr1 10 c 8 ,.,.,,., ~~~~~~~~
+chr1 11 c 8 ,.,.,,., ~~~~~~~~
+chr1 12 a 8 ,.,.,,., ~~~~~~~~
+chr1 13 a 8 ,.,.,,., ~~~~~~~~
+chr1 14 a 8 ,.,.,,., ~~~~~~~~
+chr1 15 c 8 ,.,.,,., ~~~~~~~~
+chr1 16 g 8 ,.,.,,., ~~~~~~~~
+chr1 17 t 8 ,-1t.-1T,-1t.-1T,-1t,-1t.-1T,-1t ~~~~~~~~
+chr1 18 t 8 ******** ~~~~~~~~
+chr1 19 a 8 ,.,.,,., ~~~~~~~~
+chr1 20 c 8 ,.,.,,., ~~~~~~~~
+chr1 21 g 8 ,.,.,,., ~~~~~~~~
+chr1 22 c 8 ,.,.,,., ~~~~~~~~
+chr1 23 a 8 ,.,.,,., ~~~~~~~~
+chr1 24 c 8 gGgGggGg ~~~~~~~~
+chr1 25 t 8 ,.,.,,., ~~~~~~~~
+chr1 26 c 8 ,.,.,,., ~~~~~~~~
+chr1 27 t 8 ,.,.,,., ~~~~~~~~
+chr1 28 a 8 ,.,.,,., ~~~~~~~~
+chr1 29 t 8 ,.,.,,., ~~~~~~~~
+chr1 30 g 8 ,.,.,,., ~~~~~~~~
+chr1 31 c 8 ,.,.,,., ~~~~~~~~
+chr1 32 c 8 ,.,.,,., ~~~~~~~~
+chr1 33 t 8 ,.,.,,., ~~~~~~~~
+chr1 34 g 8 ,.,.,,., ~~~~~~~~
+chr1 35 a 8 ,$.$,$.$,$,$.$,$ ~~~~~~~~
+chr1 61 t 8 ^],^],^],^],^],^],^],^], ~BBBBBBB
+chr1 62 t 8 ,,,,,,,, ~EEEEEEE
+chr1 63 g 8 ,,,,,,,, ~bbbbbbb
+chr1 64 t 8 ,,,,,,,, ~eeeeeee
+chr1 65 g 8 ,,,,,,,, ~ooooooo
+chr1 66 t 8 ,,,,,,,, ~ppppppp
+chr1 67 g 8 ,,,,,,,, ~sssssss
+chr1 68 a 8 ,,,,,,,, ~xxxxxxx
+chr1 69 c 8 ,,,,,,,, ~xxxxxxx
+chr1 70 a 8 ,,,,,,,, ~xxxxxxx
+chr1 71 c 8 ,,,,,,,, ~xxxxxxx
+chr1 72 g 8 ,,,,,,,, ~{{{{{{{
+chr1 73 c 8 ,,,,,,,, ~aaaaaaa
+chr1 74 c 8 ,,,,,,,, ~aaaaaaa
+chr1 75 g 8 ,,,,,,,, ~RRRRRRR
+chr1 76 g 8 ,,,,,,,, ~RRRRRRR
+chr1 78 g 8 ,,,,,,,, ~RRRRRRR
+chr1 79 a 8 ,,,,,,,, ~RRRRRRR
+chr1 80 t 8 ,,,,,,,, ~[[[[[[[
+chr1 81 a 8 ,,,,,,,, ~[[[[[[[
+chr1 82 g 8 ,,,,,,,, ~[[[[[[[
+chr1 83 g 8 ,,,,,,,, ~[[[[[[[
+chr1 84 g 8 aaaaaaaa ~[[[[[[[
+chr1 85 c 8 ,,,,,,,, ~[[[[[[[
+chr1 86 a 8 ,,,,,,,, ~[[[[[[[
+chr1 87 t 8 ,,,,,,,, ~iiiiiii
+chr1 88 c 8 ,,,,,,,, ~iiiiiii
+chr1 89 a 8 ,,,,,,,, ~lllllll
+chr1 90 g 8 ,,,,,,,, ~~~~~~~~
+chr1 91 c 8 ,,,,,,,, ~~~~~~~~
+chr1 92 a 8 ,,,,,,,, ~aaaaaaa
+chr1 93 a 8 ,,,,,,,, ~_______
+chr1 94 g 8 ,,,,,,,, ~UUUUUUU
+chr1 95 t 8 ,$,$,$,$,$,$,$,$ ~EEEEEEE
diff -r d2424abb9404 -r 23e5913327b4 test-data/example.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.vcf Thu Nov 05 09:57:03 2015 -0500
@@ -0,0 +1,25 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO== 15">
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FILTER=
+##FILTER=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT== 15">
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
+chr1 17 . TT T . PASS ADP=8;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:41:8:8:0:8:100%:7.77E-5:0:93:0:0:3:5
diff -r d2424abb9404 -r 23e5913327b4 tool_dependencies.xml
--- a/tool_dependencies.xml Wed Nov 19 10:04:52 2014 -0500
+++ b/tool_dependencies.xml Thu Nov 05 09:57:03 2015 -0500
@@ -1,55 +1,14 @@
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- svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ;
-
- cd samtools-parallel-mpileup ;
- cd $(ls |grep samtools-) ;
-
- sed -i 's/-lcurses/-lncurses/' Makefile ;
- sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ;
-
- make ;
- cp samtools ../samtools-parallel-mpileup
-
- samtools-parallel-mpileup/samtools-parallel-mpileup
- $INSTALL_DIR/bin
-
-
- $INSTALL_DIR/bin
- $REPOSITORY_INSTALL_DIR
-
-
-
-
- Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
-
-
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-
-
+
+
+
+
+
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+
+
+
diff -r d2424abb9404 -r 23e5913327b4 varscan_mpileup2indel.xml
--- a/varscan_mpileup2indel.xml Wed Nov 19 10:04:52 2014 -0500
+++ b/varscan_mpileup2indel.xml Thu Nov 05 09:57:03 2015 -0500
@@ -1,82 +1,86 @@
-
- VarScan2 INDEL detection; directly from a *.mpileup file.
-
- varscan
-
-
- cat $mpileup_input | java
- -Xmx64G
- -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
- mpileup2indel
-
- #if $extended_parameters.parameters == "extended"
- --min-coverage $extended_parameters.varscan_min_coverage
- --min-reads2 $extended_parameters.varscan_min_reads2
- --min-avg-qual $extended_parameters.varscan_min_avg_qual
- --min-var-freq $extended_parameters.varscan_min_var_freq
- --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
- --p-value $extended_parameters.varscan_p_value
- $extended_parameters.varscan_strand_filter
- $extended_parameters.varscan_variants
- #end if
-
- #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
- --output-vcf 1
- #end if
-
- 2> stderr.txt
- > $snv_output ;
- cat stderr.txt
-
-
-
-
-
-
-
-
-
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-
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-
+
+ VarScan2 INDEL detection; directly from a *.mpileup file.
+
+
+ varscan
+
+
+ java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1
+
+
+ cat $mpileup_input | java
+ -Xmx64G
+ -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
+ mpileup2indel
+
+ #if $extended_parameters.parameters == "extended"
+ --min-coverage $extended_parameters.varscan_min_coverage
+ --min-reads2 $extended_parameters.varscan_min_reads2
+ --min-avg-qual $extended_parameters.varscan_min_avg_qual
+ --min-var-freq $extended_parameters.varscan_min_var_freq
+ --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
+ --p-value $extended_parameters.varscan_p_value
+ $extended_parameters.varscan_strand_filter
+ $extended_parameters.varscan_variants
+ #end if
+
+ #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
+ --output-vcf 1
+ #end if
+
+ 2> stderr.txt
+ > $snv_output ;
+ cat stderr.txt
+
+
+
+
+
+
+
+
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+
+
+
+
+
**VarScan 2.3.6**
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.
@@ -105,13 +109,23 @@
* VarScan2.3.6: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0)
* parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
+Contact
+-------
-**Contact**
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-http://toolshed.dtls.nl/
+More tools by the Translational Research IT (TraIT) project can be found
+in the following toolsheds:
+
+http://toolshed.g2.bx.psu.edu/
+
+http://testtoolshed.g2.bx.psu.edu/
+
+ 10.1101/gr.129684.111
+
\ No newline at end of file
diff -r d2424abb9404 -r 23e5913327b4 varscan_mpileup2indel_from_bam.tar.xz
Binary file varscan_mpileup2indel_from_bam.tar.xz has changed
diff -r d2424abb9404 -r 23e5913327b4 varscan_mpileup2indel_from_bam.xml
--- a/varscan_mpileup2indel_from_bam.xml Wed Nov 19 10:04:52 2014 -0500
+++ b/varscan_mpileup2indel_from_bam.xml Thu Nov 05 09:57:03 2015 -0500
@@ -1,280 +1,288 @@
-
- VarScan2 INDEL detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.
-
- ncurses
- samtools_parallel_mpileup_0_1_19a
- varscan
- ncurses
- samtools
-
-
- #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
- echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
- #else
- #import os.path
- #for $alignment in $alignments
-
- #if not os.path.isfile(str($alignment)+".bai")
- echo "- Indexing alignment file: $alignment.name " ;
- samtools index $alignment 2>&1 ;
- #else
- echo "- Skiping indexing: $alignment.name " ;
- #end if
- #end for
-
- #if $mpileup_parallelization.mpileup_parallelization_select == "true"
- samtools-parallel-mpileup mpileup
- -t $mpileup_parallelization.samtools_threads
- #else
- samtools mpileup
- #end if
- -f
- #if $reference_genome_source.source_select == "indexed_filtered"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "indexed_all"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "history"
- "$reference_genome_source.reference_genome"
- #else
-
- "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
- #end if
-
- #if $extended_parameters_regions.samtools_regions == "region"
- -r $extended_parameters_regions.samtools_r
- #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
- -l $extended_parameters_regions.samtools_l
- #end if
-
- #if $extended_parameters.parameters == "extended"
- $extended_parameters.samtools_6
- $extended_parameters.samtools_A
- $extended_parameters.samtools_B
- -C $extended_parameters.samtools_C
- -d $extended_parameters.samtools_d
- $extended_parameters.samtools_E
- -M $extended_parameters.samtools_M
- $extended_parameters.samtools_R
- -q $extended_parameters.samtools_q
- -Q $extended_parameters.samtools_Q
-
- -e $extended_parameters.samtools_e
- -F $extended_parameters.samtools_F
- -h $extended_parameters.samtools_h
- $extended_parameters.samtools_I
- -L $extended_parameters.samtools_L
- -m $extended_parameters.samtools_m
- -o $extended_parameters.samtools_o
- $extended_parameters.samtools_p
- -P $extended_parameters.samtools_P
- #end if
-
- #for $alignment in $alignments
- ${alignment}
- #end for
- 2>stderr_1.txt
-
- #if $mpileup_parallelization.mpileup_parallelization_select == "true"
- #if $mpileup_parallelization.sort_mpileup
- | sort -k 1,1 -k 2,2
- #end if
- #end if
-
- | java
- -Xmx64G
- -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
- mpileup2indel
-
- #if $extended_parameters.parameters == "extended"
- --min-coverage $extended_parameters.varscan_min_coverage
- --min-reads2 $extended_parameters.varscan_min_reads2
- --min-avg-qual $extended_parameters.varscan_min_avg_qual
- --min-var-freq $extended_parameters.varscan_min_var_freq
- --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
- --p-value $extended_parameters.varscan_p_value
- $extended_parameters.varscan_strand_filter
- $extended_parameters.varscan_variants
- #end if
-
- #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
- --output-vcf 1
- #end if
-
- 2>stderr_2.txt
- > $snv_output ;
-
-
- echo "---------------[ mpileup generation ]---------------" ;
- cat stderr_1.txt ;
- echo "" ;
- echo "---------------[ VarScan INDEL detect ]---------------" ;
- cat stderr_2.txt ;
- echo "" ;
- echo "----------------------------------------------------" ;
- #end if
-
-
-
-
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-
+
+ VarScan2 INDEL detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.
+
+
+ samtools_parallel_mpileup_0_1_19a
+ samtools
+ varscan
+
+
+ java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1
+
+
+ #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
+ echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
+ #else
+ #import os.path
+ #for $alignment in $alignments
+
+ #if not os.path.isfile(str($alignment)+".bai")
+ echo "- Indexing alignment file: $alignment.name " ;
+ samtools index $alignment 2>&1 ;
+ #else
+ echo "- Skiping indexing: $alignment.name " ;
+ #end if
+ #end for
+
+ #if $mpileup_parallelization.mpileup_parallelization_select == "true"
+ samtools-parallel-mpileup mpileup
+ -t $mpileup_parallelization.samtools_threads
+ #else
+ samtools mpileup
+ #end if
+ -f
+ #if $reference_genome_source.source_select == "indexed_filtered"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "indexed_all"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "history"
+ "$reference_genome_source.reference_genome"
+ #else
+
+ "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ #end if
+
+ #if $extended_parameters_regions.samtools_regions == "region"
+ -r $extended_parameters_regions.samtools_r
+ #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
+ -l $extended_parameters_regions.samtools_l
+ #end if
+
+ #if $extended_parameters.parameters == "extended"
+ $extended_parameters.samtools_6
+ $extended_parameters.samtools_A
+ $extended_parameters.samtools_B
+ -C $extended_parameters.samtools_C
+ -d $extended_parameters.samtools_d
+ $extended_parameters.samtools_E
+ -M $extended_parameters.samtools_M
+ $extended_parameters.samtools_R
+ -q $extended_parameters.samtools_q
+ -Q $extended_parameters.samtools_Q
+
+ -e $extended_parameters.samtools_e
+ -F $extended_parameters.samtools_F
+ -h $extended_parameters.samtools_h
+ $extended_parameters.samtools_I
+ -L $extended_parameters.samtools_L
+ -m $extended_parameters.samtools_m
+ -o $extended_parameters.samtools_o
+ $extended_parameters.samtools_p
+ -P $extended_parameters.samtools_P
+ #end if
+
+ #for $alignment in $alignments
+ ${alignment}
+ #end for
+ 2>stderr_1.txt
+
+ #if $mpileup_parallelization.mpileup_parallelization_select == "true"
+ #if $mpileup_parallelization.sort_mpileup
+ | sort -k1,1V -k2,2g
+ #end if
+ #end if
+
+ | java
+ -Xmx64G
+ -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
+ mpileup2indel
+
+ #if $extended_parameters.parameters == "extended"
+ --min-coverage $extended_parameters.varscan_min_coverage
+ --min-reads2 $extended_parameters.varscan_min_reads2
+ --min-avg-qual $extended_parameters.varscan_min_avg_qual
+ --min-var-freq $extended_parameters.varscan_min_var_freq
+ --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
+ --p-value $extended_parameters.varscan_p_value
+ $extended_parameters.varscan_strand_filter
+ $extended_parameters.varscan_variants
+ #end if
+
+ #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
+ --output-vcf 1
+ #end if
+
+ 2>stderr_2.txt
+ > $snv_output ;
+
+
+ echo "---------------[ mpileup generation ]---------------" ;
+ cat stderr_1.txt ;
+ echo "" ;
+ echo "---------------[ VarScan INDEL detect ]-------------" ;
+ cat stderr_2.txt ;
+ echo "" ;
+ echo "----------------------------------------------------" ;
+ #end if
+
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+
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+
+
+
+
+
+
+
+
+
+
**VarScan 2.3.6**
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.
@@ -304,12 +312,23 @@
* parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
-**Contact**
+Contact
+-------
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-http://toolshed.dtls.nl/
-
+More tools by the Translational Research IT (TraIT) project can be found
+in the following toolsheds:
+
+http://toolshed.g2.bx.psu.edu/
+
+http://testtoolshed.g2.bx.psu.edu/
+
+
+ 10.1101/gr.129684.111
+
\ No newline at end of file