Mercurial > repos > yhoogstrate > varscan_mpileup2indel_from_bam
changeset 0:10e2ea79ec55 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
| author | yhoogstrate |
|---|---|
| date | Thu, 05 Nov 2015 10:00:19 -0500 |
| parents | |
| children | 2c56a59a112f |
| files | README.rst example.fa.1.bed example.fa.2.bed test-data/example.bam test-data/example.fa test-data/example.fa.1.bed test-data/example.fa.2.bed test-data/example.fa.fai test-data/example.mpileup test-data/example.mpileup.parallel test-data/example.vcf tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml varscan_mpileup2indel.xml varscan_mpileup2indel_from_bam.xml |
| diffstat | 16 files changed, 788 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Nov 05 10:00:19 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 <http://www.gnu.org/licenses/>.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example.fa.1.bed Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,1 @@ +chr1 0 330
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example.fa.2.bed Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,1 @@ +chr1 330 600
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.fa Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,11 @@ +>chr1 +aaataggtcccaaacgttacgcactctatgcctgacaaagttgcgaccacttcctctgcc +ttgtgtgacacgccggagatagggcatcagcaagtacgttaagtacactgaacgaactgg +aggtttctacatcgtgcgtgatggctctaggagaagtgggtgtatctgcacagcataagt +tataagacggaagtaaagcgtcttcaccgttcagcaccccacgctcatagtcaatgctgg +ttcagcatagtcaagcgccggtggcctccaaaaagacgcactgagtagcttagctacttt +gctccgcttgcggaagcactaagaggagattgaatttccaaatcccccccgatacctgtg +cggtcgctacgtaagtgcgaagttctgttagatacgctccccttagtatatgggcgttaa +tcggaccgtcggtactcactgcattccaggtctcatatagttcgccctagaagcctggga +tgaacgttgaactatagctgatgtaaaccccgcgtgccaattccaggcgtcatgggggca +acccctcgcagcctccctcttgctgttggtgcctagtatttcatgatttcgagccgacat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.fa.1.bed Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,1 @@ +chr1 0 330
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.fa.2.bed Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,1 @@ +chr1 330 600
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.fa.fai Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,1 @@ +chr1 600 6 60 61
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.mpileup Thu Nov 05 10:00:19 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.mpileup.parallel Thu Nov 05 10:00:19 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.vcf Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,25 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15"> +##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)"> +##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant"> +##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant"> +##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test"> +##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)"> +##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools_parallel_mpileup" version="0.1.19-a"> + <repository changeset_revision="7dd0c6a9be41" name="package_samtools_parallel_mpileup_0_1_19_a" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="varscan" version="2.3.6"> + <repository changeset_revision="6f8cead3dc93" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varscan_mpileup2indel.xml Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,131 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="varscan_mpileup2indel" name="VarScan2 Call INDELs from a mpileup file" version="2.3.6.a"> + <description>VarScan2 INDEL detection; directly from a *.mpileup file.</description> + + <requirements> + <requirement type="package" version="2.3.6">varscan</requirement> + </requirements> + + <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> + + <command> + 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 + </command> + + <inputs> + <param format="pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/><!-- datatype "mpileup" does not exist.. it seems to be common to use pileup instead? --> + + <conditional name="extended_parameters"> + <param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings."> + <option value="default">Default settings</option> + <option value="extended">Extended settings</option> + </param> + <when value="default"> + </when> + <when value="extended"> + <param type="integer" name="varscan_min_coverage" value="8" label="VarScan: Minimum read depth at a position to make a call [8]" /> + <param type="integer" name="varscan_min_reads2" value="2" label="VarScan: PMinimum supporting reads at a position to call variants [2]" /> + <param type="integer" name="varscan_min_avg_qual" value="15" label="VarScan: Minimum base quality at a position to count a read [15]" /> + <param type="float" name="varscan_min_var_freq" value="0.01" label="VarScan: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" /> + <param type="float" name="varscan_min_freq_for_hom" value="0.75" label="VarScan: Minimum frequency to call homozygote [0.75]" /> + <param type="float" name="varscan_p_value" value="0.99" label="VarScan: Default p-value threshold for calling variants [99e-02]" /> + <param type="boolean" name="varscan_strand_filter" falsevalue=" --strand_filter 0" truevalue=" --strand_filter 1" checked="true" label="VarScan: Ignore variants with >90% support on one strand [1]" /> + <param type="boolean" name="varscan_variants" falsevalue=" --variants 0" truevalue=" --variants 1" checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" /> + </when> + </conditional> + + <param name="varscan_output" type="select" label="Output format"> + <option value="vcf">VCF</option> + <option value="tabular">tabular</option> + </param> + </inputs> + + <outputs> + <data format="tabular" name="snv_output" label="${tool.name} on ${mpileup_input.hid}: ${mpileup_input.name}"> + <change_format> + <when input="varscan_output" value="vcf" format="vcf" /> + </change_format> + </data> + </outputs> + + <tests> + <test> + <param name="mpileup_input" value="example.mpileup" ftype="pileup" /> + <param name="parameters" value="default" /> + <param name="varscan_output_vcf" value="1" /> + + <output name="snv_output" file="example.vcf" /> + </test> + </tests> + + <help> +**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. +http://dx.doi.org/10.1101/gr.129684.111 +http://www.ncbi.nlm.nih.gov/pubmed/19542151 + +*VarScan* requires mpileup formatted input files, which are generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing it is bypassed. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan. +The samtools package is not able to parallelize the mpileup generation which make it a very slow process. +Other people were aware of this and have written a version that can do parallelization: +https://github.com/mydatascience/parallel-mpileup + +Consequently, when a BAM files gets processed by this wrapper, it's processed by *parallel-mpileup* before its send to VarScan. + +.. _VarScan: http://varscan.sourceforge.net/ + +**Input formats** + +VarScan2 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** + +Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment. + +**License** + +* 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 +------- + +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 toolsheds: + +http://toolshed.g2.bx.psu.edu/ + +http://testtoolshed.g2.bx.psu.edu/ +</help> + <citations> + <citation type="doi">10.1101/gr.129684.111</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varscan_mpileup2indel_from_bam.xml Thu Nov 05 10:00:19 2015 -0500 @@ -0,0 +1,334 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="varscan_mpileup2indel_from_bam" name="VarScan2 Call INDELs from BAM" version="2.3.6.a"> + <description>VarScan2 INDEL detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.</description> + + <requirements> + <requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="2.3.6">varscan</requirement> + </requirements> + + <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> + + <command> + #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 + <!-- @todo use the existence of $alignment.metadata.bam_index or $alignment.metadata['bam_index'] --> + #if not os.path.isfile(str($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 + <!-- + This is a workaround to obtain the "genome.fa" file that + corresponds to the dbkey of the alignments. + Because this file is "calculated" during run-time, it can + be used in a workflow. + --> + "${ 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 + </command> + + <inputs> + <param format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file(s)" help="Mapped reads in BAM or SAM format."/> + + <!-- Find out how to access the reference genome from the BAM file(s) --> + <conditional name="reference_genome_source"> + <param name="source_select" type="select" label="Fasta Source"> + <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> + <option value="history">Use reference from the history</option> + <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option> + <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option> + </param> + <when value="history"> + <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (FASTA)" help="Reference genome (genome.fa) that corresponds to the *.bam file." /> + </when> + <when value="indexed_filtered"> + <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > + <options from_data_table="all_fasta"> + <column name="name" index="2"/> + <column name="dbkey" index="1"/> + <column name="value" index="3"/><!-- Value is the path of the fasta file --> + <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" /> + <validator type="no_options" message="No indexes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="indexed_all"> + <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > + <options from_data_table="all_fasta"> + <column name="name" index="2"/> + <column name="dbkey" index="1"/> + <column name="value" index="3"/><!-- Value is the path of the fasta file --> + <validator type="no_options" message="No indexes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="attribute" /> + </conditional> + + <conditional name="extended_parameters_regions"> + <param name="samtools_regions" type="select" label="Region specific parameters" help="Let samtools target specific genomic locations."> + <option value="entire_genome">Entire genome</option> + <option value="region">Specific region</option> + <option value="regions_file_pos">Specific positions (file); list of positions</option> + <option value="regions_file_bed">Specific regions (file); list of regions in BED</option> + </param> + <when value="entire_genome" /> + <when value="region"> + <param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:pos or chr:start-end" /> + </when> + <when value="regions_file_pos"> + <param type="data" name="samtools_l" format="tabular" label="Samtools: list of positions (chr pos)" /> + </when> + <when value="regions_file_bed"> + <param type="data" name="samtools_l" format="bed" label="Samtools: specific regions (BED)" /> + </when> + </conditional> + + <conditional name="mpileup_parallelization"> + <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation (experimental)" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance."> + <option value="false" >False - uses classical samtools</option> + <option value="true">True - uses (experimental) samtools mpileup-parallel</option> + </param> + <when value="false" /> + <when value="true"> + <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" /> + <param type="boolean" name="sort_mpileup" truevalue="true" falsevalue="false" label="Sort mpileup file (SLOW)" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." /> + </when> + </conditional> + + <conditional name="extended_parameters"> + <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings."> + <option value="default">Default settings</option> + <option value="extended">Extended settings</option> + </param> + <when value="default" /> + <when value="extended"> + <param type="boolean" name="samtools_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" /> + <param type="boolean" name="samtools_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" /> + <param type="boolean" name="samtools_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" /> + <param type="integer" name="samtools_C" value="0" label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" /> + <param type="integer" name="samtools_d" value="250" label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" /> + <param type="boolean" name="samtools_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" /> + <param type="integer" name="samtools_M" value="60" label="cap mapping quality at INT [60]" /> + <param type="boolean" name="samtools_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" /> + <param type="integer" name="samtools_q" value="0" label="Samtools: skip alignments with mapQ smaller than INT [0]" /> + <param type="integer" name="samtools_Q" value="13" label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" /> + + <param type="integer" name="samtools_e" value="20" label="Samtools: Phred-scaled gap extension seq error probability [20]" /> + <param type="float" name="samtools_F" value="0.002" label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" /> + <param type="integer" name="samtools_h" value="100" label="Samtools: coefficient for homopolymer errors [100]" /> + <param type="boolean" name="samtools_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" /> + <param type="integer" name="samtools_L" value="250" label="Samtools: max per-sample depth for INDEL calling [250]" /> + <param type="integer" name="samtools_m" value="1" label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" /> + <param type="integer" name="samtools_o" value="40" label="Samtools: Phred-scaled gap open sequencing error probability [40]" /> + <param type="boolean" name="samtools_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" /> + <param type="text" name="samtools_P" value="all" label="Samtools: comma separated list of platforms for indels [all]" /> + + <param type="integer" name="varscan_min_coverage" value="8" label="VarScan: Minimum read depth at a position to make a call [8]" /> + <param type="integer" name="varscan_min_reads2" value="2" label="VarScan: PMinimum supporting reads at a position to call variants [2]" /> + <param type="integer" name="varscan_min_avg_qual" value="15" label="VarScan: Minimum base quality at a position to count a read [15]" /> + <param type="float" name="varscan_min_var_freq" value="0.01" label="VarScan: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" /> + <param type="float" name="varscan_min_freq_for_hom" value="0.75" label="VarScan: Minimum frequency to call homozygote [0.75]" /> + <param type="float" name="varscan_p_value" value="0.99" label="VarScan: Default p-value threshold for calling variants [99e-02]" /> + <param type="boolean" name="varscan_strand_filter" falsevalue=" --strand_filter 0" truevalue=" --strand_filter 1" checked="true" label="VarScan: Ignore variants with >90% support on one strand [1]" /> + <param type="boolean" name="varscan_variants" falsevalue=" --variants 0" truevalue=" --variants 1" checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" /> + </when> + </conditional> + + <param name="varscan_output" type="select" label="Output format"> + <option value="vcf">VCF</option> + <option value="tabular">tabular</option> + </param> + </inputs> + + <outputs> + <data format="tabular" name="snv_output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}"> + <change_format> + <when input="varscan_output" value="vcf" format="vcf" /> + </change_format> + </data> + </outputs> + + <tests> + <test><!-- Use classical samtools --> + <param name="alignments" value="example.bam" ftype="bam" /> + + <param name="source_select" value="history" /> + <param name="reference_genome" value="example.fa" ftype="fasta" /> + + <param name="samtools_regions" value="entire_genome" /> + + <param name="mpileup_parallelization_select" value="false" /> + <param name="sort_mpileup" value="true" /> + + <param name="parameters" value="default" /> + <param name="varscan_output_vcf" value="1" /> + + + <output name="snv_output" file="example.vcf" /> + </test> + <test><!-- Use parallelized samtools --> + <param name="alignments" value="example.bam" ftype="bam" /> + + <param name="source_select" value="history" /> + <param name="reference_genome" value="example.fa" ftype="fasta" /> + + <param name="samtools_regions" value="entire_genome" /> + + <param name="mpileup_parallelization_select" value="true" /> + <param name="samtools_threads" value="2" /> + <param name="sort_mpileup" value="true" /> + + <param name="parameters" value="default" /> + <param name="varscan_output_vcf" value="1" /> + + + <output name="snv_output" file="example.vcf" /> + </test> + </tests> + + <help> +**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. +http://dx.doi.org/10.1101/gr.129684.111 +http://www.ncbi.nlm.nih.gov/pubmed/19542151 + +*VarScan* requires mpileup formatted input files, which are generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing it is bypassed. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan. +The samtools package is not able to parallelize the mpileup generation which make it a very slow process. +Other people were aware of this and have written a version that can do parallelization: +https://github.com/mydatascience/parallel-mpileup + +Consequently, when a BAM files gets processed by this wrapper, it's processed by *parallel-mpileup* before its send to VarScan. + +.. _VarScan: http://varscan.sourceforge.net/ + +**Input formats** + +VarScan2 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** + +Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment. + +**License** + +* 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 +------- + +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 toolsheds: + +http://toolshed.g2.bx.psu.edu/ + +http://testtoolshed.g2.bx.psu.edu/ + </help> + <citations> + <citation type="doi">10.1101/gr.129684.111</citation> + </citations> +</tool> \ No newline at end of file