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Changeset 17:4c80a1387285 (2015-02-20)

Previous changeset 16:6d9407020066 (2014-12-16) Next changeset 18:28d1363f4fea (2015-03-05)

Commit message:
Uploaded

modified:
freebayes.xml
test-data/freebayes-phix174-test1.vcf
tool_dependencies.xml

added:
test-data/freebayes-phix174-test2.vcf
tool_data_table_conf.xml.sample
tool_test_output.json

removed:
tool-data/tool_data_table_conf.xml.sample

diff -r 6d9407020066 -r 4c80a1387285 freebayes.xml
--- a/freebayes.xml Tue Dec 16 16:15:43 2014 -0500
+++ b/freebayes.xml Fri Feb 20 19:02:43 2015 -0500

[

b'@@ -1,7 +1,7 @@\n <?xml version="1.0"?>\n-<tool id="freebayes" name="FreeBayes" version="0.3">\n+<tool id="freebayes" name="FreeBayes" version="0.4">\n <requirements>\n- <requirement type="package" version="0.9.18_0059bdf">freebayes</requirement>\n+ <requirement type="package" version="0_9_20_b040236">freebayes</requirement>\n <requirement type="package" version="0.1.18">samtools</requirement>\n </requirements>\n <description> - bayesian genetic variant detector</description>\n@@ -76,18 +76,49 @@\n --min-coverage "${options_type.min_coverage}"\n \n ## Command line direct text entry is not allowed at this time for security reasons\n-\n-## #elif str( $options_type.options_type_selector ) == "cline":\n- \n-## ${options_type.cline}\n- \n-## @optional_inputs_outputs@\n \n #elif str( $options_type.options_type_selector ) == "full":\n- \n-##optional inputs and outputs\n \n- @optional_inputs_outputs@\n+ #if $options_type.optional_inputs.optional_inputs_selector:\n+ \n+ #if $options_type.optional_inputs.output_trace_option:\n+ --trace "${output_trace}"\n+ #end if\n+ \n+ #if $options_type.optional_inputs.output_failed_alleles_option:\n+ --failed-alleles "${output_failed_alleles_bed}"\n+ #end if\n+ \n+ #if $options_type.optional_inputs.samples:\n+ --samples "${options_type.optional_inputs.samples}"\n+ #end if\n+ \n+ #if $options_type.optional_inputs.populations:\n+ --populations "${options_type.optional_inputs.populations}"\n+ #end if\n+ \n+ #if $options_type.optional_inputs.A:\n+ --cnv-map "${options_type.optional_inputs.A}"\n+ #end if\n+ \n+ #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":\n+ --variant-input "input_variant_vcf.vcf.gz" ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above\n+ ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}\n+ #end if\n+ \n+ #if $options_type.optional_inputs.haplotype_basis_alleles:\n+ --haplotype-basis-alleles "${options_type.optional_inputs.haplotype_basis_alleles}"\n+ #end if\n+ \n+ #if $options_type.optional_inputs.observation_bias:\n+ --observation-bias "${options_type.optional_inputs.observation_bias}"\n+ #end if\n+ \n+ #if $options_type.optional_inputs.contamination_estimates:\n+ --contamination-estimates "${options_type.optional_inputs.contamination_estimates}"\n+ #end if\n+ \n+ #end if\n \n ## REPORTING\n \n@@ -193,87 +224,6 @@\n \n </command>\n \n- <macros>\n- <token name="@optional_inputs_outputs@"> \n- ## This token gets injected in commane in two instances: when options_type.options_type_selector == "full" and "cline" ( cline is not supported at this time )\n- \n- #if $options_type.optional_inputs.optional_inputs_selector:\n- \n- #if $options_type.optional_inputs.output_trace_option:\n- --trace "${output_trace}"\n- #end if\n- \n- #if $options_type.optional_inputs.output_failed_alleles_option:\n- --failed-alleles "${output_failed_alleles_bed}"\n- #end if\n- \n- #if $options_type.optional_inputs.samples:\n- --samples "${options_type.optional_inputs.samples}"\n- #end if\n- \n- #if $options_type.optional_inputs.populations:\n- --populations "${options_type.optional_inputs.populations}"\n- #end if\n- \n- #if $options_type.optional_inputs.A:\n- --cnv-map "${options_type.optional_inputs.A}"\n- #end if\n- \n- #if str( $options_type.optional_inp'..b' <conversion name="Tabixized_input" type="tabix" />\n+ </param>\n+ <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />\n+ </when>\n+ </conditional>\n+ <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" help="--haplotype-basis-alleles" />\n+ <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False" label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes." help="--report-monomorphic " />\n+ <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from" help="--observation-bias; The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" /> \n+ <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample \'*\' can be used to set default contamination estimates." />\n+ </when>\n+ <when value="do_not_set">\n+ \n+ </when>\n+ </conditional>\n \n \n \n@@ -506,28 +487,10 @@\n \n <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " />\n </when>\n- \n- \n-\n </conditional>\n \n </inputs>\n+ \n <outputs>\n <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />\n <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">\n@@ -545,6 +508,14 @@\n <param name="options_type_selector" value="simple"/>\n <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>\n </test>\n+ <test>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>\n+ <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>\n+ <param name="options_type_selector" value="naive_w_filters"/>\n+ <param name="min_coverage" value="14"/>\n+ <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>\n+ </test>\n </tests>\n <stdio>\n <exit_code range="1:" />\n@@ -556,7 +527,7 @@\n \n See https://github.com/ekg/freebayes for details on FreeBayes.\n \n-This Galaxy instance of FreeBayes corresponds to release 0.9.18\n+This Galaxy instance of FreeBayes corresponds to release 0.9.20\n \n ------\n \n'

diff -r 6d9407020066 -r 4c80a1387285 test-data/freebayes-phix174-test1.vcf
--- a/test-data/freebayes-phix174-test1.vcf Tue Dec 16 16:15:43 2014 -0500
+++ b/test-data/freebayes-phix174-test1.vcf Fri Feb 20 19:02:43 2015 -0500

b'@@ -1,27 +1,26 @@\n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tunknown\n-phiX174\t311\t.\tA\tG\t6.48411\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPP=7.35324;RPPR=3.32051;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:478:2:70:-5.49703,0,-10\n-phiX174\t374\t.\tT\tG\t30.6931\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=7.0665;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPP=3.0103;RPPR=7.35324;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:4:2:141:2:75:-6.69903,0,-10\n-phiX174\t913\t.\tA\tC\t13.1703\t.\tAB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=29;NS=1;NUMALT=1;ODDS=2.98318;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=171;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:5:3:171:2:58:-5.00485,0,-10\n-phiX174\t1205\t.\tA\tC\t2.30262\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=0.357718;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPP=7.35324;RPPR=7.35324;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:10:8:456:2:67:-5.00791,0,-10\n-phiX174\t1245\t.\tG\tT\t6.48411\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPP=7.35324;RPPR=3.32051;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:389:2:70:-5.49703,0,-10\n-phiX174\t1249\t.\tT\tG\t15.3287\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=3.4998;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPP=3.0103;RPPR=5.80219;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:464:2:74:-5.87703,0,-10\n-phiX174\t1445\t.\tC\tA\t24.4745\t.\tAB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=5.63189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPP=3.0103;RPPR=6.91895;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:7:5:273:2:76:-6.43501,0,-10\n-phiX174\t1577\t.\tA\tC\t4.06305\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=0.437365;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPP=3.0103;RPPR=10.7656;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:460:2:60:-4.54703,0,-10\n-phiX174\t1631\t.\tT\tG\t2.719\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=0.138972;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:10:8:500:2:68:-5.10291,0,-10\n-phiX174\t1772\t.\tT\tG\t2.16317\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=0.437618;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPP=3.0103;RPPR=3.32051;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:10:7:425:2:59:-4.1670'..b'R=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=2.76444;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:5:3:150:2:57:-4.90985,0,-13.4949\n+phiX174\t3110\t.\tT\tC\t34.4848\t.\tAB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=7.94006;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:6:361:3:94:-7.98834,0,-32.3067\n+phiX174\t3155\t.\tT\tG\t23.5283\t.\tAB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=5.41314;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:7:5:299:2:75:-6.34001,0,-26.723\n+phiX174\t3325\t.\tA\tC\t5.77196\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=1.02152;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:284:2:58:-4.87991,0,-25.6399\n+phiX174\t3418\t.\tA\tC\t0.61163\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=1.88894;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/0:10:8:526:2:60:-4.34291,0,-46.6404\n+phiX174\t3729\t.\tC\tT\t8.03017\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.67776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:232:2:61:-5.16491,0,-20.8299\n+phiX174\t4031\t.\tT\tG\t23.4861\t.\tAB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=5.40338;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:8:6:322:2:85:-7.11392,0,-28.5556\n+phiX174\t4502\t.\tA\tC\t8.30185\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=1.75158;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:284:2:55:-4.59491,0,-25.6399\n+phiX174\t4558\t.\tC\tG\t6.48999\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=1.24027;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:204:2:59:-4.97491,0,-18.2399\n+phiX174\t4655\t.\tT\tG\t21.8853\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=5.03277;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:6:4:193:2:70:-6.01991,0,-17.2224\n'

diff -r 6d9407020066 -r 4c80a1387285 test-data/freebayes-phix174-test2.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174-test2.vcf Fri Feb 20 19:02:43 2015 -0500

@@ -0,0 +1,19 @@
+phiX174 1134 . A . 1.75185e-15 . DP=14;DPB=14;EPPR=3.0103;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=916;RO=14;RPPR=8.59409 GT:DP:RO:QR:AO:QA:GL 0/0:14:14:916:.:.:0
+phiX174 1135 . C . 1.75538e-15 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198 GT:DP:RO:QR:AO:QA:GL 0/0:14:14:957:.:.:0
+phiX174 1136 . G . 1.75185e-15 . DP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103 GT:DP:RO:QR:AO:QA:GL 0/0:14:14:919:.:.:0
+phiX174 1137 . C . 1.75349e-15 . DP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072 GT:DP:RO:QR:AO:QA:GL 0/0:14:14:927:.:.:0
+phiX174 1138 . C . 1.75538e-15 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198 GT:DP:RO:QR:AO:QA:GL 0/0:14:14:876:.:.:0
+phiX174 1139 . G . 1.75538e-15 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198 GT:DP:RO:QR:AO:QA:GL 0/0:14:14:946:.:.:0
+phiX174 1140 . T . 6.10945e-16 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:927:.:.:0
+phiX174 1141 . T G 0.000113755 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=10.55;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;RPPR=5.49198;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=5.49198;SRR=9;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/0:15:14:880:1:50:-1.66064,0,-76.4892
+phiX174 1142 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1082;RO=16;RPPR=3.55317 GT:DP:RO:QR:AO:QA:GL 0/0:16:16:1082:.:.:0
+phiX174 1143 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1029;RO=16;RPPR=3.55317 GT:DP:RO:QR:AO:QA:GL 0/0:16:16:1029:.:.:0
+phiX174 1144 . C . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1114;RO=16;RPPR=3.55317 GT:DP:RO:QR:AO:QA:GL 0/0:16:16:1114:.:.:0
+phiX174 1145 . G . 6.0859e-16 . DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1042;RO=15;RPPR=3.15506 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:1042:.:.:0
+phiX174 1146 . C . 6.0859e-16 . DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1058;RO=15;RPPR=3.15506 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:1058:.:.:0
+phiX174 1147 . T . 6.10945e-16 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=999;RO=15;RPPR=4.31318 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:999:.:.:0
+phiX174 1148 . C . 6.10945e-16 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1003;RO=15;RPPR=4.31318 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:1003:.:.:0
+phiX174 1149 . T C 7.90879e-06 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=13.2161;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=830;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=4.51363;SRR=8;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/0:14:13:830:1:33:-0.231708,0,-72.2702
+phiX174 1151 . C T 5.70134e-07 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=15.8459;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=946;RO=14;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=12.937;SRR=11;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/0:15:14:946:1:27:0,-0.639359,-83.1157
+phiX174 1152 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=993;RO=16;RPPR=5.18177 GT:DP:RO:QR:AO:QA:GL 0/0:16:16:993:.:.:0
+phiX174 1153 . T . 0 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=880;RO=15;RPPR=4.31318 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:880:.:.:0

diff -r 6d9407020066 -r 4c80a1387285 tool-data/tool_data_table_conf.xml.sample
--- a/tool-data/tool_data_table_conf.xml.sample Tue Dec 16 16:15:43 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-
-<tables>
-    
-    <table name="fasta_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/fasta_indexes.loc" />
-    </table>
-</tables>

diff -r 6d9407020066 -r 4c80a1387285 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Feb 20 19:02:43 2015 -0500

@@ -0,0 +1,8 @@
+
+<tables>
+    
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>

diff -r 6d9407020066 -r 4c80a1387285 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Dec 16 16:15:43 2014 -0500
+++ b/tool_dependencies.xml Fri Feb 20 19:02:43 2015 -0500

@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<tool_dependency>
-    <package name="freebayes" version="0.9.18_0059bdf">
-        <repository changeset_revision="8f3ba7808a87" name="package_freebayes_0_9_18_0059bdf" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="freebayes" version="0_9_20_b040236">
+        <repository changeset_revision="059e6e3d99cc" name="package_freebayes_0_9_20_b040236" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
         <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />

diff -r 6d9407020066 -r 4c80a1387285 tool_test_output.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_test_output.json Fri Feb 20 19:02:43 2015 -0500

[

@@ -0,0 +1,1 @@
+{"tests": [], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 0, "num_tests": 0}}
\ No newline at end of file