| Next changeset 1:162c88041ed7 (2016-05-10) |
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LICENSE filter_vcf.sh filter_vcf.xml test-data/1_short.vcf test-data/2_short.vcf test-data/test_input.vcf test-data/test_output.vcf test-data/testresult.fa tool_dependencies.xml vcfs2fasta.sh vcfs2fasta.xml |
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| diff -r 000000000000 -r cb29f95c7b88 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Mon May 09 09:27:06 2016 -0400 |
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| b'@@ -0,0 +1,676 @@\n+\n+\n+ GNU GENERAL PUBLIC LICENSE\n+ Version 3, 29 June 2007\n+\n+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>\n+ Everyone is permitted to copy and distribute verbatim copies\n+ of this license document, but changing it is not allowed.\n+\n+ Preamble\n+\n+ The GNU General Public License is a free, copyleft license for\n+software and other kinds of works.\n+\n+ The licenses for most software and other practical works are designed\n+to take away your freedom to share and change the works. By contrast,\n+the GNU General Public License is intended to guarantee your freedom to\n+share and change all versions of a program--to make sure it remains free\n+software for all its users. We, the Free Software Foundation, use the\n+GNU General Public License for most of our software; it applies also to\n+any other work released this way by its authors. You can apply it to\n+your programs, too.\n+\n+ When we speak of free software, we are referring to freedom, not\n+price. Our General Public Licenses are designed to make sure that you\n+have the freedom to distribute copies of free software (and charge for\n+them if you wish), that you receive source code or can get it if you\n+want it, that you can change the software or use pieces of it in new\n+free programs, and that you know you can do these things.\n+\n+ To protect your rights, we need to prevent others from denying you\n+these rights or asking you to surrender the rights. Therefore, you have\n+certain responsibilities if you distribute copies of the software, or if\n+you modify it: responsibilities to respect the freedom of others.\n+\n+ For example, if you distribute copies of such a program, whether\n+gratis or for a fee, you must pass on to the recipients the same\n+freedoms that you received. You must make sure that they, too, receive\n+or can get the source code. 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The systematic\n+pattern of such abuse occurs in the area of products for individuals to\n+use, which is precisely where it is most unacceptable. Therefore, we\n+have designed this version of the GPL to prohibit the practice for those\n+products. If such problems arise substantially in other domains, we\n+stand ready to extend this provision to those domains in future versions\n+of the GPL, as needed to protect the freedom of users.\n+\n+ Finally, every program is threatened constantly by software patents.\n+States should not allow patents to restrict development and use of\n+software on general-purpose computers, but in those that do, we wish to\n+avoid the special danger that patents applied to a free program could\n+make it effectively proprietary. To prevent this, the GPL assures that\n+patents cannot be used to render the program non-free.\n+\n+ The precise terms and conditions for copying, distribution and\n+modification follow.\n+\n+ TERMS AND CONDITIONS\n+\n+ 0. Definitions.\n+\n+ "This License" refers to version 3 of the GNU General Public License.\n+\n+ "Copyright" also means copyright-like laws that apply to other kinds of\n+works, such as semiconductor masks.\n+\n+ "The Program" refers '..b'CE OF THE PROGRAM\n+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\n+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n+\n+ 16. Limitation of Liability.\n+\n+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\n+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS\n+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY\n+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE\n+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF\n+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD\n+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),\n+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF\n+SUCH DAMAGES.\n+\n+ 17. Interpretation of Sections 15 and 16.\n+\n+ If the disclaimer of warranty and limitation of liability provided\n+above cannot be given local legal effect according to their terms,\n+reviewing courts shall apply local law that most closely approximates\n+an absolute waiver of all civil liability in connection with the\n+Program, unless a warranty or assumption of liability accompanies a\n+copy of the Program in return for a fee.\n+\n+ END OF TERMS AND CONDITIONS\n+\n+ How to Apply These Terms to Your New Programs\n+\n+ If you develop a new program, and you want it to be of the greatest\n+possible use to the public, the best way to achieve this is to make it\n+free software which everyone can redistribute and change under these terms.\n+\n+ To do so, attach the following notices to the program. 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If not, see <http://www.gnu.org/licenses/>.\n+\n+Also add information on how to contact you by electronic and paper mail.\n+\n+ If the program does terminal interaction, make it output a short\n+notice like this when it starts in an interactive mode:\n+\n+ {project} Copyright (C) {year} {fullname}\n+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w\'.\n+ This is free software, and you are welcome to redistribute it\n+ under certain conditions; type `show c\' for details.\n+\n+The hypothetical commands `show w\' and `show c\' should show the appropriate\n+parts of the General Public License. Of course, your program\'s commands\n+might be different; for a GUI interface, you would use an "about box".\n+\n+ You should also get your employer (if you work as a programmer) or school,\n+if any, to sign a "copyright disclaimer" for the program, if necessary.\n+For more information on this, and how to apply and follow the GNU GPL, see\n+<http://www.gnu.org/licenses/>.\n+\n+ The GNU General Public License does not permit incorporating your program\n+into proprietary programs. If your program is a subroutine library, you\n+may consider it more useful to permit linking proprietary applications with\n+the library. If this is what you want to do, use the GNU Lesser General\n+Public License instead of this License. But first, please read\n+<http://www.gnu.org/philosophy/why-not-lgpl.html>.\n' |
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| diff -r 000000000000 -r cb29f95c7b88 filter_vcf.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_vcf.sh Mon May 09 09:27:06 2016 -0400 |
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| @@ -0,0 +1,22 @@ +#!/bin/bash + +# echo $@ + +OUTPUT=$1 +shift +VCF=$1 +shift +ONLYGOOD=$1 +shift +FILTERS=$@ + +FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') + +CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT" + +if [ $ONLYGOOD != "NOTTHERE" ]; then + CMD="$CMD --only-good" +fi + +echo "CMD: "$CMD +eval $CMD |
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| diff -r 000000000000 -r cb29f95c7b88 filter_vcf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_vcf.xml Mon May 09 09:27:06 2016 -0400 |
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| @@ -0,0 +1,112 @@ +<tool id="filter_vcf" name="Filter VCF" version="1.0"> + <description>filters a VCF file</description> + <requirements> + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="package" version="0.6.8dev">pyvcf</requirement> + <requirement type="package" version="3.11">pyyaml</requirement> + <requirement type="package" version="2.0.2">bintrees</requirement> + <requirement type="package" version="1.66">biopython</requirement> + <requirement type="package" version="1.4">matplotlib</requirement> + <requirement type="package" version="0.23.1">cython</requirement> + <requirement type="package" version="1.0">phephenix</requirement> + </requirements> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command interpreter="bash"> + filter_vcf.sh + $output + $input + #if str($onlygood) == "false": + onlygood + #else + NOTTHERE + #end if + #for $sf in $snp_filter: + #for $name, $param in $sf.snp_filter_type.iteritems(): + #if $name not in [ "__current_case__", "snp_filter_type_selector" ]: + ${name}:"${param}" + #end if + #end for + #end for + </command> + + <inputs> + <param name="input" type="data" format="vcf" label="VCF File to filter" /> + + <repeat name="snp_filter" title="SNP Filter" help=""> + <conditional name="snp_filter_type"> + <param name="snp_filter_type_selector" type="select" label="SNP Filter Type"> + <option value="gq_score_option">GQ score</option> + <option value="dp4_ratio_option">DP4 ratio</option> + <option value="ad_ratio_option">AD ratio</option> + <option value="mq_score_option">MQ score</option> + <option value="min_depth_option">Minimum depth</option> + <option value="uncall_gt_option">Uncall GT</option> + <option value="mq0_ratio_option">MQ0 ratio</option> + <option value="qual_score_option">Quality score</option> + <option value="mq0f_ratio_option">MQ0F ratio</option> + </param> + <when value="gq_score_option"> + <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer"/> + </when> + <when value="dp4_ratio_option"> + <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float"/> + </when> + <when value="ad_ratio_option"> + <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float"/> + </when> + <when value="mq_score_option"> + <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer"/> + </when> + <when value="min_depth_option"> + <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer"/> + </when> + <when value="uncall_gt_option"> + <param name="uncall_gt" type="text" value="" hidden="True"/> + </when> + <when value="mq0_ratio_option"> + <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float"/> + </when> + <when value="qual_score_option"> + <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer"/> + </when> + <when value="mq0f_ratio_option"> + <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float"/> + </when> + </conditional> + </repeat> + <param name="onlygood" type="select" label="Write only good variants to output" help="Write only variants that PASS all filters. "> + <option value="true" selected="true">Write all</option> + <option value="false">Write only good</option> + </param> + </inputs> + + <outputs> + <data format="vcf" name="output" label="${tool.name} on ${on_string}: filtered VCF" /> + </outputs> + <tests> + <test> + <param name="input" value="test_input.vcf" ftype="vcf" /> + <param name="min_depth" value="100" /> + <output name="output" file="test_output.vcf" ftype="vcf" /> + </test> + </tests> + <help> + +usage: filter_vcf.py [-h] \-\-vcf VCF \-\-filters FILTERS \-\-output OUTPUT + +optional arguments: + +-h, \-\-help show this help message and exit + +\-\-vcf VCF, -v VCF VCF file to (re)filter. + +\-\-filters FILTERS, -f FILTERS Filter(s) to apply as key:threshold pairs, separated by comma. + +\-\-output OUTPUT, -o OUTPUT Location for filtered VCF to be written. + + </help> +</tool> |
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| diff -r 000000000000 -r cb29f95c7b88 test-data/1_short.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_short.vcf Mon May 09 09:27:06 2016 -0400 |
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| b'@@ -0,0 +1,50000 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##GATKCommandLine=<ID=SelectVariants,Version=2.6-5-gba531bd,Date="Thu May 22 09:24:36 BST 2014",Epoch=1400747076888,CommandLineOptions="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/input_variant.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n+##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.6-5-gba531bd,Date="Thu May 22 09:10:24 BST 2014",Epoch=1400746224902,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input_0.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOrigina'..b'.\tAN=2;DP=146;MQ=60.00;MQ0=0\tGT:DP\t0/0:146\n+gi|15829254|ref|NC_002695.1|\t49922\t.\tT\t.\t434.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49923\t.\tC\t.\t434.23\t.\tAN=2;DP=143;MQ=60.00;MQ0=0\tGT:DP\t0/0:143\n+gi|15829254|ref|NC_002695.1|\t49924\t.\tA\t.\t428.23\t.\tAN=2;DP=141;MQ=60.00;MQ0=0\tGT:DP\t0/0:141\n+gi|15829254|ref|NC_002695.1|\t49925\t.\tA\t.\t440.23\t.\tAN=2;DP=149;MQ=60.00;MQ0=0\tGT:DP\t0/0:149\n+gi|15829254|ref|NC_002695.1|\t49926\t.\tT\t.\t440.23\t.\tAN=2;DP=152;MQ=60.00;MQ0=0\tGT:DP\t0/0:152\n+gi|15829254|ref|NC_002695.1|\t49927\t.\tG\t.\t446.23\t.\tAN=2;DP=155;MQ=60.00;MQ0=0\tGT:DP\t0/0:155\n+gi|15829254|ref|NC_002695.1|\t49928\t.\tT\t.\t452.23\t.\tAN=2;DP=157;MQ=60.00;MQ0=0\tGT:DP\t0/0:157\n+gi|15829254|ref|NC_002695.1|\t49929\t.\tC\t.\t443.23\t.\tAN=2;DP=153;MQ=60.00;MQ0=0\tGT:DP\t0/0:153\n+gi|15829254|ref|NC_002695.1|\t49930\t.\tG\t.\t449.23\t.\tAN=2;DP=155;MQ=60.00;MQ0=0\tGT:DP\t0/0:155\n+gi|15829254|ref|NC_002695.1|\t49931\t.\tA\t.\t449.23\t.\tAN=2;DP=156;MQ=60.00;MQ0=0\tGT:DP\t0/0:156\n+gi|15829254|ref|NC_002695.1|\t49932\t.\tT\t.\t461.23\t.\tAN=2;DP=159;MQ=60.00;MQ0=0\tGT:DP\t0/0:159\n+gi|15829254|ref|NC_002695.1|\t49933\t.\tG\t.\t449.23\t.\tAN=2;DP=156;MQ=60.00;MQ0=0\tGT:DP\t0/0:156\n+gi|15829254|ref|NC_002695.1|\t49934\t.\tA\t.\t455.23\t.\tAN=2;DP=156;MQ=60.00;MQ0=0\tGT:DP\t0/0:156\n+gi|15829254|ref|NC_002695.1|\t49935\t.\tA\t.\t452.23\t.\tAN=2;DP=156;MQ=60.00;MQ0=0\tGT:DP\t0/0:156\n+gi|15829254|ref|NC_002695.1|\t49936\t.\tG\t.\t455.23\t.\tAN=2;DP=158;MQ=60.00;MQ0=0\tGT:DP\t0/0:157\n+gi|15829254|ref|NC_002695.1|\t49937\t.\tA\t.\t440.23\t.\tAN=2;DP=155;MQ=60.00;MQ0=0\tGT:DP\t0/0:155\n+gi|15829254|ref|NC_002695.1|\t49938\t.\tG\t.\t449.23\t.\tAN=2;DP=157;MQ=60.00;MQ0=0\tGT:DP\t0/0:157\n+gi|15829254|ref|NC_002695.1|\t49939\t.\tC\t.\t443.23\t.\tAN=2;DP=155;MQ=60.00;MQ0=0\tGT:DP\t0/0:155\n+gi|15829254|ref|NC_002695.1|\t49940\t.\tA\t.\t440.23\t.\tAN=2;DP=154;MQ=60.00;MQ0=0\tGT:DP\t0/0:154\n+gi|15829254|ref|NC_002695.1|\t49941\t.\tT\t.\t449.23\t.\tAN=2;DP=155;MQ=60.00;MQ0=0\tGT:DP\t0/0:155\n+gi|15829254|ref|NC_002695.1|\t49942\t.\tC\t.\t446.23\t.\tAN=2;DP=155;MQ=60.00;MQ0=0\tGT:DP\t0/0:155\n+gi|15829254|ref|NC_002695.1|\t49943\t.\tC\t.\t428.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49944\t.\tG\t.\t428.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49945\t.\tC\t.\t431.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49946\t.\tA\t.\t425.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49947\t.\tC\t.\t431.23\t.\tAN=2;DP=145;MQ=60.00;MQ0=0\tGT:DP\t0/0:145\n+gi|15829254|ref|NC_002695.1|\t49948\t.\tA\t.\t404.23\t.\tAN=2;DP=137;MQ=60.00;MQ0=0\tGT:DP\t0/0:137\n+gi|15829254|ref|NC_002695.1|\t49949\t.\tT\t.\t425.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:143\n+gi|15829254|ref|NC_002695.1|\t49950\t.\tT\t.\t419.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49951\t.\tG\t.\t431.23\t.\tAN=2;DP=146;MQ=60.00;MQ0=0\tGT:DP\t0/0:146\n+gi|15829254|ref|NC_002695.1|\t49952\t.\tT\t.\t437.23\t.\tAN=2;DP=146;MQ=60.00;MQ0=0\tGT:DP\t0/0:146\n+gi|15829254|ref|NC_002695.1|\t49953\t.\tT\t.\t428.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49954\t.\tG\t.\t434.23\t.\tAN=2;DP=146;MQ=60.00;MQ0=0\tGT:DP\t0/0:146\n+gi|15829254|ref|NC_002695.1|\t49955\t.\tT\t.\t428.23\t.\tAN=2;DP=146;MQ=60.00;MQ0=0\tGT:DP\t0/0:146\n+gi|15829254|ref|NC_002695.1|\t49956\t.\tG\t.\t434.23\t.\tAN=2;DP=146;MQ=60.00;MQ0=0\tGT:DP\t0/0:146\n+gi|15829254|ref|NC_002695.1|\t49957\t.\tA\t.\t428.23\t.\tAN=2;DP=144;MQ=60.00;MQ0=0\tGT:DP\t0/0:144\n+gi|15829254|ref|NC_002695.1|\t49958\t.\tA\t.\t416.23\t.\tAN=2;DP=140;MQ=60.00;MQ0=0\tGT:DP\t0/0:140\n+gi|15829254|ref|NC_002695.1|\t49959\t.\tA\t.\t407.23\t.\tAN=2;DP=138;MQ=60.00;MQ0=0\tGT:DP\t0/0:138\n+gi|15829254|ref|NC_002695.1|\t49960\t.\tG\t.\t395.23\t.\tAN=2;DP=136;MQ=60.00;MQ0=0\tGT:DP\t0/0:136\n+gi|15829254|ref|NC_002695.1|\t49961\t.\tC\t.\t404.23\t.\tAN=2;DP=136;MQ=60.00;MQ0=0\tGT:DP\t0/0:136\n+gi|15829254|ref|NC_002695.1|\t49962\t.\tC\t.\t392.23\t.\tAN=2;DP=134;MQ=60.00;MQ0=0\tGT:DP\t0/0:134\n+gi|15829254|ref|NC_002695.1|\t49963\t.\tG\t.\t398.23\t.\tAN=2;DP=134;MQ=60.00;MQ0=0\tGT:DP\t0/0:134\n+gi|15829254|ref|NC_002695.1|\t49964\t.\tA\t.\t398.23\t.\tAN=2;DP=136;MQ=60.00;MQ0=0\tGT:DP\t0/0:136\n' |
| b |
| diff -r 000000000000 -r cb29f95c7b88 test-data/2_short.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_short.vcf Mon May 09 09:27:06 2016 -0400 |
| [ |
| b'@@ -0,0 +1,50000 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##GATKCommandLine=<ID=SelectVariants,Version=2.6-5-gba531bd,Date="Thu May 22 09:15:54 BST 2014",Epoch=1400746554393,CommandLineOptions="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-4mpB9s/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/phengs/galaxy/database/tmp/tmp-gatk-4mpB9s/input_variant.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n+##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.6-5-gba531bd,Date="Thu May 22 09:06:54 BST 2014",Epoch=1400746014908,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/phengs/galaxy/database/tmp/tmp-gatk-Gz3f1A/gatk_input_0.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-Gz3f1A/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOrigina'..b'AN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49921\t.\tT\t.\t157.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n+gi|15829254|ref|NC_002695.1|\t49922\t.\tT\t.\t157.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49923\t.\tC\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49924\t.\tA\t.\t151.23\t.\tAN=2;DP=45;MQ=60.00;MQ0=0\tGT:DP\t0/0:45\n+gi|15829254|ref|NC_002695.1|\t49925\t.\tA\t.\t163.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n+gi|15829254|ref|NC_002695.1|\t49926\t.\tT\t.\t160.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n+gi|15829254|ref|NC_002695.1|\t49927\t.\tG\t.\t160.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n+gi|15829254|ref|NC_002695.1|\t49928\t.\tT\t.\t160.23\t.\tAN=2;DP=52;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n+gi|15829254|ref|NC_002695.1|\t49929\t.\tC\t.\t160.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n+gi|15829254|ref|NC_002695.1|\t49930\t.\tG\t.\t163.23\t.\tAN=2;DP=53;MQ=60.00;MQ0=0\tGT:DP\t0/0:53\n+gi|15829254|ref|NC_002695.1|\t49931\t.\tA\t.\t166.23\t.\tAN=2;DP=54;MQ=60.00;MQ0=0\tGT:DP\t0/0:54\n+gi|15829254|ref|NC_002695.1|\t49932\t.\tT\t.\t169.23\t.\tAN=2;DP=55;MQ=60.00;MQ0=0\tGT:DP\t0/0:55\n+gi|15829254|ref|NC_002695.1|\t49933\t.\tG\t.\t163.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n+gi|15829254|ref|NC_002695.1|\t49934\t.\tA\t.\t166.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n+gi|15829254|ref|NC_002695.1|\t49935\t.\tA\t.\t169.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n+gi|15829254|ref|NC_002695.1|\t49936\t.\tG\t.\t169.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n+gi|15829254|ref|NC_002695.1|\t49937\t.\tA\t.\t163.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n+gi|15829254|ref|NC_002695.1|\t49938\t.\tG\t.\t160.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n+gi|15829254|ref|NC_002695.1|\t49939\t.\tC\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49940\t.\tA\t.\t151.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49941\t.\tT\t.\t157.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n+gi|15829254|ref|NC_002695.1|\t49942\t.\tC\t.\t160.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n+gi|15829254|ref|NC_002695.1|\t49943\t.\tC\t.\t157.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49944\t.\tG\t.\t157.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49945\t.\tC\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49946\t.\tA\t.\t154.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49947\t.\tC\t.\t154.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49948\t.\tA\t.\t151.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n+gi|15829254|ref|NC_002695.1|\t49949\t.\tT\t.\t151.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n+gi|15829254|ref|NC_002695.1|\t49950\t.\tT\t.\t148.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n+gi|15829254|ref|NC_002695.1|\t49951\t.\tG\t.\t154.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n+gi|15829254|ref|NC_002695.1|\t49952\t.\tT\t.\t157.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n+gi|15829254|ref|NC_002695.1|\t49953\t.\tT\t.\t154.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n+gi|15829254|ref|NC_002695.1|\t49954\t.\tG\t.\t157.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49955\t.\tT\t.\t151.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n+gi|15829254|ref|NC_002695.1|\t49956\t.\tG\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49957\t.\tA\t.\t151.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49958\t.\tA\t.\t148.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49959\t.\tA\t.\t148.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n+gi|15829254|ref|NC_002695.1|\t49960\t.\tG\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n+gi|15829254|ref|NC_002695.1|\t49961\t.\tC\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n+gi|15829254|ref|NC_002695.1|\t49962\t.\tC\t.\t148.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n+gi|15829254|ref|NC_002695.1|\t49963\t.\tG\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n+gi|15829254|ref|NC_002695.1|\t49964\t.\tA\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n' |
| b |
| diff -r 000000000000 -r cb29f95c7b88 test-data/test_input.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_input.vcf Mon May 09 09:27:06 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1000 @@\n+##fileformat=VCFv4.1\n+##GATKCommandLine=<ID=SelectVariants,Version=2.6-5-gba531bd,Date="Thu May 22 09:24:36 BST 2014",Epoch=1400747076888,CommandLineOptions="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/input_variant.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n+##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.6-5-gba531bd,Date="Thu May 22 09:10:24 BST 2014",Epoch=1400746224902,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input_0.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=STRICT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=6 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree='..b'MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227782\t.\tA\t.\t.\tmq_score:50\tDP=92;MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227783\t.\tG\t.\t.\tmq_score:50\tDP=91;MQ=0.0;MQ0=91\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227784\t.\tG\t.\t.\tmq_score:50\tDP=91;MQ=0.0;MQ0=91\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227785\t.\tT\t.\t.\tmq_score:50\tDP=91;MQ=0.0;MQ0=91\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227786\t.\tG\t.\t.\tmq_score:50\tDP=90;MQ=0.0;MQ0=90\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227787\t.\tT\t.\t.\tmq_score:50\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227788\t.\tA\t.\t.\tmq_score:50\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227789\t.\tG\t.\t.\tmq_score:50\tDP=88;MQ=0.0;MQ0=88\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227790\t.\tC\t.\t.\tmq_score:50\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227791\t.\tG\t.\t.\tmq_score:50\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227792\t.\tG\t.\t.\tmq_score:50\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227793\t.\tT\t.\t.\tmq_score:50\tDP=84;MQ=0.0;MQ0=84\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227794\t.\tG\t.\t.\tmq_score:50\tDP=84;MQ=0.0;MQ0=84\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227795\t.\tA\t.\t.\tmq_score:50\tDP=89;MQ=0.0;MQ0=89\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227796\t.\tA\t.\t.\tmq_score:50\tDP=89;MQ=0.0;MQ0=89\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227797\t.\tA\t.\t.\tmq_score:50\tDP=92;MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227798\t.\tT\t.\t.\tmq_score:50\tDP=89;MQ=0.0;MQ0=89\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227799\t.\tG\t.\t.\tmq_score:50\tDP=93;MQ=0.0;MQ0=93\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227800\t.\tC\t.\t.\tmq_score:50\tDP=93;MQ=0.0;MQ0=93\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227801\t.\tG\t.\t.\tmq_score:50\tDP=92;MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227802\t.\tT\t.\t.\tmq_score:50\tDP=91;MQ=0.0;MQ0=91\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227803\t.\tA\t.\t.\tmq_score:50\tDP=92;MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227804\t.\tG\t.\t.\tmq_score:50\tDP=94;MQ=0.0;MQ0=94\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227805\t.\tA\t.\t.\tmq_score:50\tDP=96;MQ=0.0;MQ0=96\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227806\t.\tG\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227807\t.\tA\t.\t.\tmq_score:50\tDP=109;MQ=0.0;MQ0=109\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227808\t.\tT\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227809\t.\tC\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227810\t.\tT\t.\t.\tmq_score:50\tDP=103;MQ=0.0;MQ0=103\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227811\t.\tG\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227812\t.\tG\t.\t.\tmq_score:50\tDP=105;MQ=0.0;MQ0=105\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227813\t.\tA\t.\t.\tmq_score:50\tDP=105;MQ=0.0;MQ0=105\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227814\t.\tG\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227815\t.\tG\t.\t.\tmq_score:50\tDP=106;MQ=0.0;MQ0=106\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227816\t.\tA\t.\t.\tmq_score:50\tDP=102;MQ=0.0;MQ0=102\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227817\t.\tA\t.\t.\tmq_score:50\tDP=102;MQ=0.0;MQ0=102\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227818\t.\tT\t.\t.\tmq_score:50\tDP=103;MQ=0.0;MQ0=103\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227819\t.\tA\t.\t.\tmq_score:50\tDP=103;MQ=0.0;MQ0=103\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227820\t.\tC\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227821\t.\tC\t.\t.\tmq_score:50\tDP=97;MQ=0.0;MQ0=97\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227822\t.\tG\t.\t.\tmq_score:50\tDP=99;MQ=0.0;MQ0=99\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227823\t.\tG\t.\t.\tmq_score:50\tDP=97;MQ=0.0;MQ0=97\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227824\t.\tT\t.\t.\tmq_score:50\tDP=95;MQ=0.0;MQ0=95\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227825\t.\tG\t.\t.\tmq_score:50\tDP=95;MQ=0.0;MQ0=95\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227826\t.\tG\t.\t.\tmq_score:50\tDP=95;MQ=0.0;MQ0=95\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227827\t.\tC\t.\t.\tmq_score:50\tDP=94;MQ=0.0;MQ0=94\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227828\t.\tG\t.\t.\tmq_score:50\tDP=94;MQ=0.0;MQ0=94\tGT\t./.\n' |
| b |
| diff -r 000000000000 -r cb29f95c7b88 test-data/test_output.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output.vcf Mon May 09 09:27:06 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1001 @@\n+##fileformat=VCFv4.1\n+##GATKCommandLine=<ID=SelectVariants,Version=2.6-5-gba531bd,Date="Thu May 22 09:24:36 BST 2014",Epoch=1400747076888,CommandLineOptions="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/input_variant.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n+##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.6-5-gba531bd,Date="Thu May 22 09:10:24 BST 2014",Epoch=1400746224902,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input_0.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=STRICT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=6 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree='..b'6\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=90;MQ=0.0;MQ0=90\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227787\t.\tT\t.\t.\tmq_score:50;min_depth:100\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227788\t.\tA\t.\t.\tmq_score:50;min_depth:100\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227789\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=88;MQ=0.0;MQ0=88\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227790\t.\tC\t.\t.\tmq_score:50;min_depth:100\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227791\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227792\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=87;MQ=0.0;MQ0=87\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227793\t.\tT\t.\t.\tmq_score:50;min_depth:100\tDP=84;MQ=0.0;MQ0=84\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227794\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=84;MQ=0.0;MQ0=84\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227795\t.\tA\t.\t.\tmq_score:50;min_depth:100\tDP=89;MQ=0.0;MQ0=89\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227796\t.\tA\t.\t.\tmq_score:50;min_depth:100\tDP=89;MQ=0.0;MQ0=89\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227797\t.\tA\t.\t.\tmq_score:50;min_depth:100\tDP=92;MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227798\t.\tT\t.\t.\tmq_score:50;min_depth:100\tDP=89;MQ=0.0;MQ0=89\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227799\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=93;MQ=0.0;MQ0=93\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227800\t.\tC\t.\t.\tmq_score:50;min_depth:100\tDP=93;MQ=0.0;MQ0=93\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227801\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=92;MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227802\t.\tT\t.\t.\tmq_score:50;min_depth:100\tDP=91;MQ=0.0;MQ0=91\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227803\t.\tA\t.\t.\tmq_score:50;min_depth:100\tDP=92;MQ=0.0;MQ0=92\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227804\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=94;MQ=0.0;MQ0=94\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227805\t.\tA\t.\t.\tmq_score:50;min_depth:100\tDP=96;MQ=0.0;MQ0=96\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227806\t.\tG\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227807\t.\tA\t.\t.\tmq_score:50\tDP=109;MQ=0.0;MQ0=109\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227808\t.\tT\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227809\t.\tC\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227810\t.\tT\t.\t.\tmq_score:50\tDP=103;MQ=0.0;MQ0=103\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227811\t.\tG\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227812\t.\tG\t.\t.\tmq_score:50\tDP=105;MQ=0.0;MQ0=105\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227813\t.\tA\t.\t.\tmq_score:50\tDP=105;MQ=0.0;MQ0=105\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227814\t.\tG\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227815\t.\tG\t.\t.\tmq_score:50\tDP=106;MQ=0.0;MQ0=106\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227816\t.\tA\t.\t.\tmq_score:50\tDP=102;MQ=0.0;MQ0=102\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227817\t.\tA\t.\t.\tmq_score:50\tDP=102;MQ=0.0;MQ0=102\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227818\t.\tT\t.\t.\tmq_score:50\tDP=103;MQ=0.0;MQ0=103\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227819\t.\tA\t.\t.\tmq_score:50\tDP=103;MQ=0.0;MQ0=103\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227820\t.\tC\t.\t.\tmq_score:50\tDP=104;MQ=0.0;MQ0=104\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227821\t.\tC\t.\t.\tmq_score:50;min_depth:100\tDP=97;MQ=0.0;MQ0=97\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227822\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=99;MQ=0.0;MQ0=99\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227823\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=97;MQ=0.0;MQ0=97\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227824\t.\tT\t.\t.\tmq_score:50;min_depth:100\tDP=95;MQ=0.0;MQ0=95\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227825\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=95;MQ=0.0;MQ0=95\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227826\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=95;MQ=0.0;MQ0=95\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227827\t.\tC\t.\t.\tmq_score:50;min_depth:100\tDP=94;MQ=0.0;MQ0=94\tGT\t./.\n+gi|15829254|ref|NC_002695.1|\t227828\t.\tG\t.\t.\tmq_score:50;min_depth:100\tDP=94;MQ=0.0;MQ0=94\tGT\t./.\n' |
| b |
| diff -r 000000000000 -r cb29f95c7b88 test-data/testresult.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testresult.fa Mon May 09 09:27:06 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>1_short +TTCTTCATGA +>2_short +TTTTACACGA +>reference +CCCATAGCAG |
| b |
| diff -r 000000000000 -r cb29f95c7b88 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 09 09:27:06 2016 -0400 |
| b |
| @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="python" version="2.7.10"> + <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pyvcf" version="0.6.8dev"> + <repository changeset_revision="7ef691e979b5" name="package_python_2_7_pyvcf_0_6_8dev" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> + <package name="pyyaml" version="3.11"> + <repository changeset_revision="99267d131c05" name="package_python_2_7_pyyaml_3_11" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> + <package name="cython" version="0.23.1"> + <repository changeset_revision="65f6ba2786d0" name="package_python_2_7_10_cython_0_23_1" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> + <package name="bintrees" version="2.0.2"> + <repository changeset_revision="618a0c8a468b" name="package_python_2_7_bintrees_2_0_2" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> + <package name="biopython" version="1.66"> + <repository changeset_revision="c722591ee0aa" name="package_python_2_7_biopython_1_66" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> + <package name="matplotlib" version="1.4"> + <repository changeset_revision="f7424e1cf115" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> + <package name="phephenix" version="1.0"> + <repository changeset_revision="6690a962e75e" name="package_phephenix_1_0" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r cb29f95c7b88 vcfs2fasta.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfs2fasta.sh Mon May 09 09:27:06 2016 -0400 |
| [ |
| @@ -0,0 +1,48 @@ +#!/bin/bash + +echo $@ + +OUTPUT=$1 +shift +WITHMIXTURES=$1 +shift +COLUMNNS=$1 +shift +SAMPLENS=$1 +shift +REFERENCE=$1 +shift +INCLUDE=$1 +shift +EXCLUDE=$1 +shift +INPUT=$@ + +CMD="phenix.py vcf2fasta --out $OUTPUT --input $INPUT" + +if [ $WITHMIXTURES != "NOTTHERE" ]; then + CMD="$CMD --with-mixtures $WITHMIXTURES" +fi + +if [ $COLUMNNS != "NOTTHERE" ]; then + CMD="$CMD --column-Ns $COLUMNNS" +fi + +if [ $SAMPLENS != "NOTTHERE" ]; then + CMD="$CMD --sample-Ns $SAMPLENS" +fi + +if [ $REFERENCE != "NOTTHERE" ]; then + CMD="$CMD --reference $REFERENCE" +fi + +if [ $INCLUDE != "NOTTHERE" ]; then + CMD="$CMD --include INCLUDE" +fi + +if [ $EXCLUDE != "NOTTHERE" ]; then + CMD="$CMD --exclude EXCLUDE" +fi + +echo $CMD +eval $CMD |
| b |
| diff -r 000000000000 -r cb29f95c7b88 vcfs2fasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfs2fasta.xml Mon May 09 09:27:06 2016 -0400 |
| b |
| @@ -0,0 +1,125 @@ +<tool id="vcfs2fasta" name="VCFs to fasta" version="1.0"> + <description>Takes a set of VCF files and outputs a multi fasta file with only the variant positions.</description> + <requirements> + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="package" version="0.6.8dev">pyvcf</requirement> + <requirement type="package" version="3.11">pyyaml</requirement> + <requirement type="package" version="2.0.2">bintrees</requirement> + <requirement type="package" version="1.66">biopython</requirement> + <requirement type="package" version="1.4">matplotlib</requirement> + <requirement type="package" version="0.23.1">cython</requirement> + <requirement type="package" version="1.0">phephenix</requirement> + </requirements> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command interpreter="bash"> + vcfs2fasta.sh + $output + #if str($mix_cond.mix) == "yes": + $mix_cond.mix_value + #else + NOTTHERE + #end if + #if str($cols_cond.cols) == "yes": + $cols_cond.column_ns + #else + NOTTHERE + #end if + #if str($sample_cond.sample) == "yes": + $sample_cond.sample_ns + #else + NOTTHERE + #end if + #if str($reference_cond.reference) == "yes": + $reference_cond.ref_fa + #else + NOTTHERE + #end if + #if str($include_cond.include) == "yes": + $include_cond.in_bed + #else + NOTTHERE + #end if + #if str($exclude_cond.exclude) == "yes": + $exclude_cond.ex_bed + #else + NOTTHERE + #end if + #for $i, $input_vcf in enumerate( $input_vcfs ): + "${input_vcf}" + #end for + </command> + + <inputs> + <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" /> + <conditional name="mix_cond"> + <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="mix_value" type="float" value="0.5" label="Mixture value" /> + </when> + </conditional> + <conditional name="cols_cond"> + <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns above specified threshold."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="column_ns" type="float" value="0.5" label="Column Ns value" /> + </when> + </conditional> + <conditional name="sample_cond"> + <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns above specified threshold."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" /> + </when> + </conditional> + <conditional name="reference_cond"> + <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/> + </when> + </conditional> + <conditional name="include_cond"> + <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/> + </when> + </conditional> + <conditional name="exclude_cond"> + <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/> + </when> + </conditional> + </inputs> + + <outputs> + <data format="fasta" name="output" label="${tool.name} on ${on_string}: FASTA file" /> + </outputs> + <test> + <param name="input_vcfs" value="1_short.vcf" ftype="vcf" /> + <param name="input_vcfs" value="2_short.vcf" ftype="vcf" /> + <output name="output" file="testresult.fa" ftype="fasta" /> + </test> + <help> + + </help> +</tool> |