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Changeset 7:7adfd0589f49 (2017-04-18)

Previous changeset 6:20f0429a4bfe (2016-12-19) Next changeset 8:ce135864629c (2017-10-24)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1

modified:
readme.rst
snpEff.xml
snpEff_databases.xml
snpEff_download.xml
snpEff_macros.xml

added:
test-data/input.vcf

removed:
test-data/vcf_homhet.vcf
tool_dependencies.xml

diff -r 20f0429a4bfe -r 7adfd0589f49 readme.rst
--- a/readme.rst Mon Dec 19 11:56:53 2016 -0500
+++ b/readme.rst Tue Apr 18 09:33:56 2017 -0400

@@ -6,14 +6,6 @@

.. _SnpEff: http://snpeff.sourceforge.net/

-
-This repository let you automatically install SnpEff and SnpSift.
-This will use the default location for genome reference downloads from the ``snpEff.config`` file:
-
- data_dir = ~/snpEff/data/
-
-You can manually edit the installed ``snpEff.config`` file and change the location, or you can create a symbolic link to the desired data location from ``~/snpEff``.
-
The genome reference options used by the tools "SnpEff" (snpEff.xml) and "SnpEff Download" (snpEff_download.xml) are taken from the ``tool-data/snpeffect_genomedb.loc`` file.
You can fill this file by running the following command:

@@ -35,4 +27,3 @@
.. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/

Wrapper authors: Jim Johnson
-

diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff.xml
--- a/snpEff.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff.xml Tue Apr 18 09:33:56 2017 -0400

[

b'@@ -6,23 +6,20 @@\n <expand macro="requirements" />\n <expand macro="stdio" />\n <expand macro="version_command" />\n- <command>\n-<![CDATA[\n- @CONDA_SNPEFF_JAR_PATH@ &&\n- java -Xmx6G -jar "\\$SNPEFF_JAR_PATH/snpEff.jar" eff\n- -c "\\$SNPEFF_JAR_PATH/snpEff.config"\n+ <command><![CDATA[\n+ snpEff -Xmx8g eff\n -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength\n #if $spliceSiteSize and str($spliceSiteSize) != \'\':\n -spliceSiteSize "$spliceSiteSize"\n #end if\n #if $spliceRegion.setSpliceRegions == \'yes\':\n- #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != \'\':\n+ #if str($spliceRegion.spliceRegionExonSize)\n -spliceRegionExonSize $spliceRegion.spliceRegionExonSize\n #end if\n- #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != \'\':\n+ #if str($spliceRegion.spliceRegionIntronMin)\n -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin\n #end if\n- #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != \'\':\n+ #if str($spliceRegion.spliceRegionIntronMax)\n -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax\n #end if\n #end if\n@@ -39,63 +36,63 @@\n -no $eff\n #end for\n #end if\n- #if str( $transcripts ) != \'None\':\n- -onlyTr $transcripts\n+ #if $transcripts\n+ -onlyTr \'$transcripts\'\n #end if\n- #if str( $intervals ) != \'None\': ### fix this for multiple dataset input\n- -interval $intervals\n+ #if $intervals ### fix this for multiple dataset input\n+ -interval \'$intervals\'\n #end if\n #if $statsFile:\n- -stats $statsFile\n+ -stats \'$statsFile\'\n #end if\n #if str($offset) != \'default\':\n ${offset}\n #end if\n #if str($chr).strip() != \'\':\n- -chr "$chr"\n+ -chr \'$chr\'\n #end if\n $noLog\n+ ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites\n+ ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes\n #if $snpDb.genomeSrc == \'cached\':\n -dataDir ${snpDb.genomeVersion.fields.path}\n- #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != \'\':\n- #echo " "\n- #echo \' \'.join(str($snpDb.extra_annotations).split(\',\'))\n- #end if\n- #if $snpDb.regulation and str($snpDb.regulation) != \'\':\n- -reg #echo \' -reg \'.join(str($snpDb.regulation).split(\',\'))#\n+ #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != \'\':\n+ #set $regs = [x for x in str($snpDb.reg_section.regulation).split(\',\')]\n+ #for reg in $regs:\n+ -reg \'"${reg}"\'\n+ #end for\n #end if\n $snpDb.genomeVersion\n #elif $snpDb.genomeSrc == \'history\':\n- -dataDir ${snpDb.snpeff_db.extra_files_path}\n- #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != \'\':\n- #set xannotations = [\' \'] + str($snpDb.extra_annotations).split(\',\')\n- #echo " "\n- #echo \' -\'.join($xannotations)\n+ -dataDir \'${snpDb.snpeff_db.extra_files_path}\'\n+ #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != \'\':\n+ #set $regs = [x for x in str($snpDb.reg_section.regulation).split(\',\')]\n+ #for reg in $regs:\n+ -reg \'"${reg}"\'\n+ #end for\n #end if\n- #if $snpDb.regulation and str($snpDb.regulation) != \'\':\n- -reg #echo \' -reg \'.join(str($snpDb.regulation).split(\',\'))#\n- #end if\n- ${snpDb.snpeff_db.metadata.genome_version}\n+ \'${snpDb.snpeff_db.'..b'tional.outputFormat" value="bedAnn" format="bed" />\n </change_format>\n </data>\n- <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">\n+ <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats">\n <filter>generate_stats == True</filter>\n </data>\n </outputs>\n <tests>\n- \n- \n- \n- \n-\n- <test>\n- <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>\n- <param name="inputFormat" value="vcf"/>\n- <param name="outputFormat" value="vcf"/>\n- <param name="genomeSrc" value="named"/>\n- <param name="genome_version" value="testCase"/>\n- <param name="udLength" value="0"/>\n- \n- <param name="generate_stats" value="False"/>\n- <output name="snpeff_output">\n- <assert_contents>\n- \n- <has_text_matching expression="Y\\t59030478\\t.*intergenic_region" />\n- \n- <has_text_matching expression="Y\\t59032947\\t.*\\tGT" />\n- </assert_contents>\n- </output>\n- </test>\n-\n- \n- \n-\n </tests>\n <help><![CDATA[\n-\n This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.\n \n @EXTERNAL_DOCUMENTATION@\n-\n ]]>\n </help>\n <expand macro="citations" />\n </tool>\n-\n'

diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff_databases.xml
--- a/snpEff_databases.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_databases.xml Tue Apr 18 09:33:56 2017 -0400

[

@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0">
+<tool id="snpEff_databases" name="SnpEff available databases" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -6,12 +6,9 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-<![CDATA[
-    @CONDA_SNPEFF_JAR_PATH@ &&
-    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > "$snpeff_dbs"
-]]>
-    </command>
+    <command><![CDATA[
+snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/  *//g' > '$snpeff_dbs'
+    ]]></command>
     <inputs>
     </inputs>
     <outputs>
@@ -27,11 +24,8 @@
         </test>
     </tests>
     <help><![CDATA[
-
@EXTERNAL_DOCUMENTATION@
-
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
</tool>

diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff_download.xml
--- a/snpEff_download.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_download.xml Tue Apr 18 09:33:56 2017 -0400

[

@@ -6,14 +6,11 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-<![CDATA[
-    @CONDA_SNPEFF_JAR_PATH@ &&
-    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version"
-]]>
-    </command>
+    <command><![CDATA[
+snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version'
+    ]]></command>
     <inputs>
-        <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
+        <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)">
             <help>@SNPEFF_DATABASE_URL@</help>
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
@@ -32,11 +29,7 @@
         </test>
     </tests>
     <help><![CDATA[
-
@EXTERNAL_DOCUMENTATION@
-
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
</tool>
-

diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff_macros.xml
--- a/snpEff_macros.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_macros.xml Tue Apr 18 09:33:56 2017 -0400

[

@@ -1,7 +1,7 @@
<macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
+            <requirement type="package" version="4.3k">snpeff</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,22 +10,16 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
-  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
   <xml name="version_command">
     <version_command><![CDATA[
-    if [ -z "$SNPEFF_JAR_PATH" ]; then
-        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
-    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
+snpEff -version
     ]]></version_command>
   </xml>
-  <token name="@WRAPPER_VERSION@">4.1</token>
-  <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
-  <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token>
+  <token name="@WRAPPER_VERSION@">4.3k</token>
+  <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
+  <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
-
-For details about this tool, please go to:
- http://snpeff.sourceforge.net/SnpEff_manual.html
-
+For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html
   </token>
   <xml name="citations">
       <citations>

diff -r 20f0429a4bfe -r 7adfd0589f49 test-data/input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.vcf Tue Apr 18 09:33:56 2017 -0400

b'@@ -0,0 +1,60 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diff -r 20f0429a4bfe -r 7adfd0589f49 test-data/vcf_homhet.vcf
--- a/test-data/vcf_homhet.vcf Mon Dec 19 11:56:53 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,60 +0,0 @@\n-##fileformat=VCFv4.0\n-##samtoolsVersion=0.1.15 (r949:203)\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n-##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">\n-##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">\n-##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">\n-##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">\n-##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">\n-##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">\n-##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">\n-##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">\n-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n-##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">\n-##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">\n-##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">\n-##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">\n-##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">\n-##FORMAT=<ID=PL,Number=.,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">\n-##source_20110319.1=/wsu/home/eq/eq83/eq8302/tools/vcftools/bin//vcf-merge s_1_ACAGTGA.vcf.gz s_1_CAGATCA.vcf.gz s_1_CGATGTA.vcf.gz s_1_CTTGTAA.vcf.gz s_1_GCCAATA.vcf.gz s_1_TGACCAA.vcf.gz\n-##sourceFiles_20110319.1=0:s_1_ACAGTGA.vcf.gz,1:s_1_CAGATCA.vcf.gz,2:s_1_CGATGTA.vcf.gz,3:s_1_CTTGTAA.vcf.gz,4:s_1_GCCAATA.vcf.gz,5:s_1_TGACCAA.vcf.gz\n-##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">\n-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">\n-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ts_1_ACAGTGA_sort.bam\ts_1_CAGATCA_sort.bam\ts_1_CGATGTA_sort.bam\ts_1_CTTGTAA_sort.bam\ts_1_GCCAATA_sort.bam\ts_1_TGACCAA_sort.bam\n-Y\t3718196\t.\tC\tT\t7.59\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=4.617e-16,8.575e-07,1;MQ=39;SF=1\tGT:GQ:PL\t.\t1/1:61:38,6,0\t.\t.\t.\t.\n-Y\t3720217\t.\tA\tG\t8.65\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=2;FQ=-30;G3=4.415e-15,5.291e-06,1;MQ=38;SF=5\tGT:GQ:PL\t.\t.\t.\t.\t.\t1/1:53:38,3,0\n-Y\t3720581\t.\tA\tG\t7.80\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-30;G3=5.56e-15,5.291e-06,1;MQ=44;SF=1\tGT:GQ:PL\t.\t1/1:53:37,3,0\t.\t.\t.\t.\n-Y\t3721154\t.\tA\tG\t13.90\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=9.194e-17,8.566e-07,1;MQ=37;SF=3\tGT:GQ:PL\t.\t.\t.\t1/1:61:45,6,0\t.\t.\n-Y\t3721230\t.\tC\tG\t21.80\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.456e-17,8.564e-07,1;MQ=29;SF=3\tGT:GQ:PL\t.\t.\t.\t1/1:61:53,6,0\t.\t.\n-Y\t3744605\t.\tC\tA\t3.98\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.468e-15,8.599e-07,1;MQ=19;SF=2\tGT:GQ:PL\t.\t.\t1/1:61:33,6,0\t.\t.\t.\n-Y\t4433091\t.\tT\tC\t11.10\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=1.835e-16,8.568e-07,1;MQ=23;SF=5\tGT:GQ:PL\t.\t.\t.\t.\t.\t1/1:61:42,6,0\n-Y\t9945223\t.\tATTT\tATTTT\t19.80\t.\tAC=4;AF1=1;AN=4;CI95='..b',11,0,6;DP=34;FQ=32.5;G3=1.991e-14,1,7.924e-52;INDEL;MQ=35;PV4=0.28,0.049,0.14,0.2;SF=1,3,4,5\tGT:GQ:PL\t.\t0/0:70:67,0,254\t.\t1/1:99:152,0,255\t1/1:83:80,0,255\t1/1:89:86,0,255\n-Y\t10011930\t.\tACT\tA\t90.85\t.\tAC=2;AF1=0.5;AN=4;CI95=0.5,0.5;DP4=2,6,1,3;DP=17;FQ=16.6;G3=3.155e-11,1,1.991e-34;INDEL;MQ=35;PV4=1,0.00044,0.33,1;SF=0,5\tGT:GQ:PL\t0/0:54:51,0,167\t.\t.\t.\t.\t0/0:99:206,0,255\n-Y\t10011935\t.\tC\tCT\t83.83\t.\tAC=3;AF1=0.5;AN=6;CI95=0.5,0.5;DP4=1,8,2,5;DP=23;FQ=90.3;G3=1.256e-28,1,5e-26;INDEL;MQ=39;PV4=0.55,1,0.15,1;SF=1,2,4\tGT:GQ:PL\t.\t0/0:99:138,0,125\t1/1:92:89,0,148\t.\t1/1:99:138,0,171\t.\n-Y\t10011966\t.\tATT\tAT\t79.38\t.\tAC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=1,6,0,2;DP=14;FQ=5.09;G3=1.991e-12,1,1.256e-28;INDEL;MQ=38;PV4=1,1,0.46,0.088;SF=0,1,2,3,4,5\tGT:GQ:PL\t1/1:41:38,0,92\t1/1:76:73,0,109\t1/1:99:181,0,109\t1/1:99:114,0,103\t1/1:99:139,0,171\t1/1:99:155,0,144\n-Y\t10028061\t.\tCA\tCAA\t28.40\t.\tAC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,2,1;DP=9;FQ=-43.5;G3=2.739e-22,5.886e-08,1;INDEL;MQ=37;SF=4,5\tGT:GQ:PL\t.\t.\t.\t.\t1/1:72:83,9,0\t0/0:61:52,6,0\n-Y\t10029194\t.\tCA\tC\t73.47\t.\tAC=10;AF1=0.7304;AN=12;CI95=0.5,1;DP4=2,0,7,3;DP=19;FQ=-32.5;G3=2.922e-150,0.9991,0.000854;INDEL;MQ=25;PV4=1,0.4,1,0.23;SF=0,1,2,3,4,5\tGT:GQ:PL\t0/0:3:93,0,2\t1/1:85:100,17,0\t1/1:99:181,36,0\t1/1:90:107,18,0\t1/1:3:104,0,2\t1/1:70:90,10,0\n-Y\t10029452\t.\tCAA\tCAAA\t7.26\t.\tAC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,4,0;DP=13;FQ=-46.5;G3=2.341e-18,6.106e-08,1;INDEL;MQ=26;SF=3,4\tGT:GQ:PL\t.\t.\t.\t1/1:72:50,12,0\t1/1:72:42,12,0\t.\n-Y\t10037877\t.\tGCCC\tGCCCC\t14.40\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=3;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2\tGT:GQ:PL\t.\t.\t1/1:61:53,6,0\t.\t.\t.\n-Y\t13266272\t.\tTTTT\tTTTTATTT\t51.50\t.\tAC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=5,1,7,0;DP=15;FQ=54.5;G3=7.924e-19,1,3.155e-24;INDEL;MQ=30;PV4=0.46,1,0.078,0.00035;SF=3\tGT:GQ:PL\t.\t.\t.\t0/0:92:89,0,116\t.\t.\n-Y\t13268110\t.\tGC\tGCC\t3.66\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.911e-16,8.571e-07,1;INDEL;MQ=23;SF=2\tGT:GQ:PL\t.\t.\t1/1:61:40,6,0\t.\t.\t.\n-Y\t13292082\t.\tTCCCCCCCCCC\tTCCCCCCC\t14.40\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=3\tGT:GQ:PL\t.\t.\t.\t1/1:61:53,6,0\t.\t.\n-Y\t13297070\t.\tAGGTGGTGGTGGT\tAGGTGGTGGT\t12.70\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=1;FQ=-37.5;G3=2.782e-16,5.287e-06,1;INDEL;MQ=50;SF=5\tGT:GQ:PL\t.\t.\t.\t.\t.\t1/1:53:50,3,0\n-Y\t13312198\t.\tCGGGGG\tCGGGG\t14.87\t.\tAC=5;AF1=1;AN=6;CI95=0.5,1;DP4=2,0,10,0;DP=12;FQ=-43.5;G3=1.373e-19,5.886e-08,1;INDEL;MQ=24;PV4=1,0.44,1,0.019;SF=1,4,5\tGT:GQ:PL\t.\t1/1:72:56,9,0\t.\t.\t1/1:70:57,10,0\t1/1:44:48,0,42\n-Y\t13312608\t.\tCA\tCAA\t22.50\t.\tAC=1;AF1=0.5032;AN=2;CI95=0.5,0.5;DP4=2,0,7,0;DP=16;FQ=-15.6;G3=4.937e-25,1,1.272e-08;INDEL;MQ=24;PV4=1,1,0.093,1;SF=2\tGT:GQ:PL\t.\t.\t0/0:22:60,0,19\t.\t.\t.\n-Y\t13402810\t.\tTAGAGA\tTAGA\t29.80\t.\tAC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,1;DP=2;FQ=-40.5;G3=7.299e-19,8.564e-07,1;INDEL;MQ=33;SF=0,2\tGT:GQ:PL\t1/1:61:66,6,0\t.\t1/1:72:72,9,0\t.\t.\t.\n-Y\t21153016\t.\tAG\tATG\t213.83\t.\tAC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,6,9;DP=15;FQ=-79.5;G3=7.905e-54,1e-18,1;INDEL;MQ=43;SF=0,1,2,3,4,5\tGT:GQ:PL\t1/1:99:255,45,0\t1/1:99:.,.,0\t1/1:99:255,87,0\t1/1:99:.,.,0\t1/1:99:255,78,0\t1/1:99:.,.,0\n-Y\t21153067\t.\tCCA\tC\t46.50\t.\tAC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=8,4,5,0;DP=18;FQ=49.5;G3=7.924e-18,1,5e-52;INDEL;MQ=39;PV4=0.26,0.08,0.035,1;SF=3\tGT:GQ:PL\t.\t.\t.\t0/0:87:84,0,255\t.\t.\n-Y\t26325233\t.\tTGAGAGAGAGAGA\tTGAGAGAGAGA\t22.20\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.308e-18,8.564e-07,1;INDEL;MQ=33;SF=0\tGT:GQ:PL\t1/1:61:61,6,0\t.\t.\t.\t.\t.\n-Y\t28588049\t.\tACATCAT\tACAT\t7.35\t.\tAC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-37.5;G3=1.108e-15,5.288e-06,1;INDEL;MQ=44;SF=1,3\tGT:GQ:PL\t.\t1/1:53:44,3,0\t.\t1/1:53:44,3,0\t.\t.\n-Y\t59030478\t.\tAAAACAAACAAACAAACAAACAAACAAA\tAAAACAAACAAACAAA\t14.40\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2\tGT:GQ:PL\t.\t.\t1/1:61:53,6,0\t.\t.\t.\n-Y\t59032947\t.\tGTT\tGTTT\t28.20\t.\tAC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=5.798e-19,8.564e-07,1;INDEL;MQ=37;SF=5\tGT:GQ:PL\t.\t.\t.\t.\t.\t1/1:61:67,6,0\n'

diff -r 20f0429a4bfe -r 7adfd0589f49 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Dec 19 11:56:53 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="snpEff" version="4.1">
-        <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>