Repository 'vcfflatten'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten

Changeset 0:38d93ca9c0f0 (2015-03-19)
Next changeset 1:1336a70f5c02 (2016-09-15)
Commit message:
Uploaded
added:
macros.xml
test-data/vcfflatten-input1.vcf
test-data/vcfflatten-test1.vcf
tool_dependencies.xml
vcfflatten.xml
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diff -r 000000000000 -r 38d93ca9c0f0 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Mar 19 14:31:30 2015 -0400
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@@ -0,0 +1,28 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" />
+        </stdio>
+    </xml>
+    <xml name="citations">
+         <citations>
+             <citation type="bibtex">
+@misc{Garrison2015,
+  author = {Garrison, Erik},
+  year = {2015},
+  title = {vcflib},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/ekg/vcflib},
+}
+             </citation>
+         </citations>
+    </xml>
+    <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token>
+</macros>
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diff -r 000000000000 -r 38d93ca9c0f0 test-data/vcfflatten-input1.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfflatten-input1.vcf Thu Mar 19 14:31:30 2015 -0400
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b'@@ -0,0 +1,121 @@\n+##fileformat=VCFv4.1\n+##fileDate=20140610\n+##source=Dan\n+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa\n+##filter="AF > .001"\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tgroupA\tgroupB\n+phiX174\t1015\t.\tA\tC\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0,2:0,0.2:A=8,C=2,G=1,\t0:0,0:0,0:A=26,G=1,\n+phiX174\t1016\t.\tA\tT\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0:0:A=10,\t0:2:0.0769230769231:A=24,T=2,\n+phiX174\t1038\t.\tA\tC\t0\t.\tAC=2;AF=0.046511627907\tGT:AC:AF:NC\t0:2:0.153846153846:A=11,C=2,\t0:0:0:A=30,\n+phiX174\t1045\t.\tT\tG\t0\t.\tAC=2;AF=0.0425531914894\tGT:AC:AF:NC\t0:0:0:T=15,G=1,\t0:2:0.0625:T=30,G=2,\n+phiX174\t1048\t.\tC\tA\t0\t.\tAC=2;AF=0.0434782608696\tGT:AC:AF:NC\t0:2:0.133333333333:A=2,C=13,\t0:0:0:C=31,G=1,\n+phiX174\t1050\t.\tA\tC\t0\t.\tAC=3;AF=0.0714285714286\tGT:AC:AF:NC\t0:0:0:A=12,\t0:3:0.1:A=27,C=3,\n+phiX174\t1051\t.\tT\tG\t0\t.\tAC=2;AF=0.0487804878049\tGT:AC:AF:NC\t0:2:0.166666666667:C=1,T=10,G=2,\t0:0:0:T=29,G=1,\n+phiX174\t1054\t.\tT\tG\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:2:0.153846153846:T=11,G=2,\t0:0:0:T=31,G=1,\n+phiX174\t1076\t.\tG\tC\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,G=17,\t0:0:0:G=36,\n+phiX174\t1080\t.\tG\tC\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,T=1,G=17,\t0:0:0:C=1,G=39,\n+phiX174\t1092\t.\tT\tG\t0\t.\tAC=2;AF=0.0263157894737\tGT:AC:AF:NC\t0:2:0.0833333333333:C=1,T=22,G=2,\t0:0:0:T=52,G=1,\n+phiX174\t1093\t.\tT\tG\t0\t.\tAC=2;AF=0.025974025974\tGT:AC:AF:NC\t0:2:0.08:T=23,G=2,\t0:0:0:T=52,\n+phiX174\t1102\t.\tT\tC\t0\t.\tAC=6;AF=0.0779220779221\tGT:AC:AF:NC\t0:2:0.0869565217391:C=2,T=21,\t0:4:0.0740740740741:C=4,T=50,\n+phiX174\t1107\t.\tT\tG\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:0:0:T=22,G=1,\t0:2:0.04:T=48,G=2,\n+phiX174\t1110\t.\tT\tC\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:2:0.125:C=2,T=14,\t0:0:0:C=1,T=56,G=1,\n+phiX174\t1121\t.\tT\tG\t0\t.\tAC=3;AF=0.041095890411\tGT:AC:AF:NC\t0:0:0:T=19,\t0:3:0.0555555555556:T=51,G=3,\n+phiX174\t1124\t.\tT\tC\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0,2:0,0.117647058824:C=2,T=15,G=1,\t0:0,0:0,0:T=48,G=1,\n+phiX174\t1125\t.\tT\tG\t0\t.\tAC=3;AF=0.0454545454545\tGT:AC:AF:NC\t0:3:0.176470588235:T=14,G=3,\t0:0:0:T=49,G=1,\n+phiX174\t1131\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0952380952381:T=19,G=2,\t0:0:0:T=57,\n+phiX174\t1141\t.\tT\tG\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:0:0:T=20,G=1,\t0:2:0.0338983050847:T=57,G=2,\n+phiX174\t1145\t.\tG\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,G=19,\t0:0:0:G=52,\n+phiX174\t1147\t.\tT\tC\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,T=19,\t0:0:0:T=50,\n+phiX174\t1149\t.\tT\tG,C\t0\t.\tAC=2,2;AF=0.027027027027,0.027027027027\tGT:AC:AF:NC\t0:2,2:0.1,0.1:C=2,T=16,G=2,\t0:0,0:0,0:T=54,\n+phiX174\t1156\t.\tT\tG\t0\t.\tAC=2;AF=0.031746031746\tGT:AC:AF:NC\t0:0:0:C=1,T=15,\t0:2:0.0416666666667:T=46,G=2,\n+phiX174\t1159\t.\tT\tC,G\t0\t.\tAC=2,2;AF=0.0298507462687,0.0298507462687\tGT:AC:AF:NC\t0:2,0:0.111111111111,0:C=2,T=16,\t0:0,2:0,0.0408163265306:C=1,T=47,G=2,\n+phiX174\t1164\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:0:0:C=1,T=16,G=1,\t0:4:0.0909090909091:T=40,G=4,\n+phiX174\t1168\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:2:0.0952380952381:C=1,T=19,G=2,\t0:2:0.0512820512821:T=37,G=2,\n+phiX174\t1171\t.\tT\tG\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:T=21,G=2,\t0:0:0:T=38,G=1,\n+phiX174\t1174\t.\tC\tA\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:A=2,C=21,\t0:0:0:A=1,C=38,\n+phiX174\t1178\t.\tG\tC\t0\t.\tAC=2;AF=0.03076923076'..b'7907:C=2,T=41,G=1,\n+phiX174\t1347\t.\tA\tC\t0\t.\tAC=2;AF=0.0243902439024\tGT:AC:AF:NC\t0:2:0.0512820512821:A=37,C=2,G=1,\t0:0:0:A=43,\n+phiX174\t1348\t.\tT\tG\t0\t.\tAC=2;AF=0.0240963855422\tGT:AC:AF:NC\t0:2:0.05:T=38,G=2,\t0:0:0:T=43,\n+phiX174\t1352\t.\tA\tT\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:0:0:A=34,G=1,\t0:2:0.0512820512821:A=37,T=2,\n+phiX174\t1354\t.\tT\tG,A\t0\t.\tAC=2,2;AF=0.027027027027,0.027027027027\tGT:AC:AF:NC\t0:2,0:0.0526315789474,0:T=36,G=2,\t0:0,2:0,0.0555555555556:A=2,T=34,G=1,\n+phiX174\t1359\t.\tT\tG\t0\t.\tAC=3;AF=0.0405405405405\tGT:AC:AF:NC\t0:3:0.0714285714286:T=39,G=3,\t0:0:0:T=32,G=1,\n+phiX174\t1366\t.\tG\tC\t0\t.\tAC=3;AF=0.0428571428571\tGT:AC:AF:NC\t0:3:0.0714285714286:C=3,T=1,G=39,\t0:0:0:G=28,\n+phiX174\t1370\t.\tT\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:0:0:C=1,T=45,G=1,\t0:2:0.0833333333333:A=1,T=22,G=2,\n+phiX174\t1373\t.\tT\tG\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:2:0.0408163265306:T=47,G=2,\t0:0:0:T=25,\n+phiX174\t1380\t.\tG\tC\t0\t.\tAC=2;AF=0.0238095238095\tGT:AC:AF:NC\t0:0,2:0,0.0384615384615:C=2,T=1,G=50,\t0:0,0:0,0:T=1,G=32,\n+phiX174\t1381\t.\tT\tG\t0\t.\tAC=3;AF=0.0361445783133\tGT:AC:AF:NC\t0:3:0.0576923076923:A=1,T=49,G=3,\t0:0:0:T=31,\n+phiX174\t1384\t.\tT\tG\t0\t.\tAC=4;AF=0.0512820512821\tGT:AC:AF:NC\t0:4:0.0816326530612:T=45,G=4,\t0:0:0:T=29,G=1,\n+phiX174\t1385\t.\tT\tG\t0\t.\tAC=4;AF=0.0512820512821\tGT:AC:AF:NC\t0:4:0.0816326530612:T=45,G=4,\t0:0:0:C=1,T=29,\n+phiX174\t1391\t.\tA\tC\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:2:0.0408163265306:A=47,C=2,\t0:0:0:A=30,C=1,\n+phiX174\t1393\t.\tC\tA\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:2:0.0425531914894:A=2,C=45,\t0:0:0:C=32,\n+phiX174\t1396\t.\tT\tG\t0\t.\tAC=3;AF=0.04\tGT:AC:AF:NC\t0:3:0.0697674418605:T=40,G=3,\t0:0:0:T=32,\n+phiX174\t1397\t.\tA\tC\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:0:0:A=42,T=1,\t0:2:0.0625:A=30,C=2,\n+phiX174\t1400\t.\tA\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.047619047619:A=40,C=2,G=1,\t0:0:0:A=31,\n+phiX174\t1401\t.\tA\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.047619047619:A=40,C=2,\t0:0:0:A=31,\n+phiX174\t1434\t.\tC\tT\t0\t.\tAC=2;AF=0.0571428571429\tGT:AC:AF:NC\t0:2:0.142857142857:C=12,T=2,\t0:0:0:C=21,\n+phiX174\t1438\t.\tG\tC\t0\t.\tAC=2;AF=0.0526315789474\tGT:AC:AF:NC\t0:0:0:G=15,\t0:2:0.0869565217391:C=2,G=21,\n+phiX174\t1450\t.\tT\tG\t0\t.\tAC=3;AF=0.0789473684211\tGT:AC:AF:NC\t0:3:0.176470588235:A=1,C=1,T=14,G=3,\t0:0:0:T=21,G=1,\n+phiX174\t1459\t.\tT\tG\t0\t.\tAC=3;AF=0.075\tGT:AC:AF:NC\t0:3:0.142857142857:C=1,T=18,G=3,\t0:0:0:T=19,\n+phiX174\t1470\t.\tC\tA\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:0:0:C=29,\t0:2:0.0869565217391:A=2,C=21,\n+phiX174\t1484\t.\tC\tG\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:2:0.0740740740741:A=1,C=25,G=2,\t0:0:0:C=25,\n+phiX174\t1487\t.\tT\tG\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.0689655172414:T=27,G=2,\t0:0:0:T=26,\n+phiX174\t1491\t.\tG\tT\t0\t.\tAC=2;AF=0.037037037037\tGT:AC:AF:NC\t0:0:0:T=1,G=26,\t0:2:0.0714285714286:T=2,G=26,\n+phiX174\t1503\t.\tA\tC\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:0:0:A=20,C=1,\t0:2:0.0833333333333:A=22,C=2,\n+phiX174\t1536\t.\tA\tC\t0\t.\tAC=3;AF=0.0545454545455\tGT:AC:AF:NC\t0:3:0.111111111111:A=24,C=3,\t0:0:0:A=28,C=1,\n+phiX174\t1541\t.\tT\tG\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.0740740740741:T=25,G=2,\t0:0:0:T=28,\n+phiX174\t1553\t.\tA\tG\t0\t.\tAC=2;AF=0.0408163265306\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=1,G=2,\t0:0:0:A=28,\n+phiX174\t1566\t.\tC\tG\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0:0:C=30,T=1,\t0:2:0.0571428571429:C=33,G=2,\n+phiX174\t1572\t.\tT\tG\t0\t.\tAC=2;AF=0.03125\tGT:AC:AF:NC\t0:2:0.0625:T=30,G=2,\t0:0:0:T=32,\n+phiX174\t1574\t.\tG\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0882352941176:C=3,G=31,\t0:0:0:G=34,\n+phiX174\t1575\t.\tA\tC\t0\t.\tAC=2;AF=0.0294117647059\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=33,T=1,\n+phiX174\t1577\t.\tA\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:0:0:A=35,\t0:3:0.0909090909091:A=30,C=3,\n+phiX174\t1581\t.\tT\tG\t0\t.\tAC=2;AF=0.0285714285714\tGT:AC:AF:NC\t0:2:0.0555555555556:C=1,T=34,G=2,\t0:0:0:T=34,G=1,\n+phiX174\t1591\t.\tA\tC\t0\t.\tAC=3;AF=0.037037037037\tGT:AC:AF:NC\t0:3:0.0789473684211:A=35,C=3,\t0:0:0:A=43,C=1,\n+phiX174\t1597\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0606060606061:T=31,G=2,\t0:0:0:C=1,T=45,\n'
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diff -r 000000000000 -r 38d93ca9c0f0 test-data/vcfflatten-test1.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfflatten-test1.vcf Thu Mar 19 14:31:30 2015 -0400
b
b'@@ -0,0 +1,121 @@\n+##fileformat=VCFv4.1\n+##fileDate=20140610\n+##source=Dan\n+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa\n+##filter="AF > .001"\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tgroupA\tgroupB\n+phiX174\t1015\t.\tA\tC\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0,2:0,0.2:A=8,C=2,G=1,\t0:0,0:0,0:A=26,G=1,\n+phiX174\t1016\t.\tA\tT\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0:0:A=10,\t0:2:0.0769230769231:A=24,T=2,\n+phiX174\t1038\t.\tA\tC\t0\t.\tAC=2;AF=0.046511627907\tGT:AC:AF:NC\t0:2:0.153846153846:A=11,C=2,\t0:0:0:A=30,\n+phiX174\t1045\t.\tT\tG\t0\t.\tAC=2;AF=0.0425531914894\tGT:AC:AF:NC\t0:0:0:T=15,G=1,\t0:2:0.0625:T=30,G=2,\n+phiX174\t1048\t.\tC\tA\t0\t.\tAC=2;AF=0.0434782608696\tGT:AC:AF:NC\t0:2:0.133333333333:A=2,C=13,\t0:0:0:C=31,G=1,\n+phiX174\t1050\t.\tA\tC\t0\t.\tAC=3;AF=0.0714285714286\tGT:AC:AF:NC\t0:0:0:A=12,\t0:3:0.1:A=27,C=3,\n+phiX174\t1051\t.\tT\tG\t0\t.\tAC=2;AF=0.0487804878049\tGT:AC:AF:NC\t0:2:0.166666666667:C=1,T=10,G=2,\t0:0:0:T=29,G=1,\n+phiX174\t1054\t.\tT\tG\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:2:0.153846153846:T=11,G=2,\t0:0:0:T=31,G=1,\n+phiX174\t1076\t.\tG\tC\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,G=17,\t0:0:0:G=36,\n+phiX174\t1080\t.\tG\tC\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,T=1,G=17,\t0:0:0:C=1,G=39,\n+phiX174\t1092\t.\tT\tG\t0\t.\tAC=2;AF=0.0263157894737\tGT:AC:AF:NC\t0:2:0.0833333333333:C=1,T=22,G=2,\t0:0:0:T=52,G=1,\n+phiX174\t1093\t.\tT\tG\t0\t.\tAC=2;AF=0.025974025974\tGT:AC:AF:NC\t0:2:0.08:T=23,G=2,\t0:0:0:T=52,\n+phiX174\t1102\t.\tT\tC\t0\t.\tAC=6;AF=0.0779220779221\tGT:AC:AF:NC\t0:2:0.0869565217391:C=2,T=21,\t0:4:0.0740740740741:C=4,T=50,\n+phiX174\t1107\t.\tT\tG\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:0:0:T=22,G=1,\t0:2:0.04:T=48,G=2,\n+phiX174\t1110\t.\tT\tC\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:2:0.125:C=2,T=14,\t0:0:0:C=1,T=56,G=1,\n+phiX174\t1121\t.\tT\tG\t0\t.\tAC=3;AF=0.041095890411\tGT:AC:AF:NC\t0:0:0:T=19,\t0:3:0.0555555555556:T=51,G=3,\n+phiX174\t1124\t.\tT\tC\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0,2:0,0.117647058824:C=2,T=15,G=1,\t0:0,0:0,0:T=48,G=1,\n+phiX174\t1125\t.\tT\tG\t0\t.\tAC=3;AF=0.0454545454545\tGT:AC:AF:NC\t0:3:0.176470588235:T=14,G=3,\t0:0:0:T=49,G=1,\n+phiX174\t1131\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0952380952381:T=19,G=2,\t0:0:0:T=57,\n+phiX174\t1141\t.\tT\tG\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:0:0:T=20,G=1,\t0:2:0.0338983050847:T=57,G=2,\n+phiX174\t1145\t.\tG\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,G=19,\t0:0:0:G=52,\n+phiX174\t1147\t.\tT\tC\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,T=19,\t0:0:0:T=50,\n+phiX174\t1149\t.\tT\tC\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:2,2:0.1,0.1:C=2,T=16,G=2,\t0:0,0:0,0:T=54,\n+phiX174\t1156\t.\tT\tG\t0\t.\tAC=2;AF=0.031746031746\tGT:AC:AF:NC\t0:0:0:C=1,T=15,\t0:2:0.0416666666667:T=46,G=2,\n+phiX174\t1159\t.\tT\tG\t0\t.\tAC=2;AF=0.0298507462687\tGT:AC:AF:NC\t0:2,0:0.111111111111,0:C=2,T=16,\t0:0,2:0,0.0408163265306:C=1,T=47,G=2,\n+phiX174\t1164\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:0:0:C=1,T=16,G=1,\t0:4:0.0909090909091:T=40,G=4,\n+phiX174\t1168\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:2:0.0952380952381:C=1,T=19,G=2,\t0:2:0.0512820512821:T=37,G=2,\n+phiX174\t1171\t.\tT\tG\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:T=21,G=2,\t0:0:0:T=38,G=1,\n+phiX174\t1174\t.\tC\tA\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:A=2,C=21,\t0:0:0:A=1,C=38,\n+phiX174\t1178\t.\tG\tC\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:2:0.0740740740741:C=2,'..b'\t0:0,2:0,0.046511627907:C=2,T=41,G=1,\n+phiX174\t1347\t.\tA\tC\t0\t.\tAC=2;AF=0.0243902439024\tGT:AC:AF:NC\t0:2:0.0512820512821:A=37,C=2,G=1,\t0:0:0:A=43,\n+phiX174\t1348\t.\tT\tG\t0\t.\tAC=2;AF=0.0240963855422\tGT:AC:AF:NC\t0:2:0.05:T=38,G=2,\t0:0:0:T=43,\n+phiX174\t1352\t.\tA\tT\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:0:0:A=34,G=1,\t0:2:0.0512820512821:A=37,T=2,\n+phiX174\t1354\t.\tT\tA\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:2,0:0.0526315789474,0:T=36,G=2,\t0:0,2:0,0.0555555555556:A=2,T=34,G=1,\n+phiX174\t1359\t.\tT\tG\t0\t.\tAC=3;AF=0.0405405405405\tGT:AC:AF:NC\t0:3:0.0714285714286:T=39,G=3,\t0:0:0:T=32,G=1,\n+phiX174\t1366\t.\tG\tC\t0\t.\tAC=3;AF=0.0428571428571\tGT:AC:AF:NC\t0:3:0.0714285714286:C=3,T=1,G=39,\t0:0:0:G=28,\n+phiX174\t1370\t.\tT\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:0:0:C=1,T=45,G=1,\t0:2:0.0833333333333:A=1,T=22,G=2,\n+phiX174\t1373\t.\tT\tG\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:2:0.0408163265306:T=47,G=2,\t0:0:0:T=25,\n+phiX174\t1380\t.\tG\tC\t0\t.\tAC=2;AF=0.0238095238095\tGT:AC:AF:NC\t0:0,2:0,0.0384615384615:C=2,T=1,G=50,\t0:0,0:0,0:T=1,G=32,\n+phiX174\t1381\t.\tT\tG\t0\t.\tAC=3;AF=0.0361445783133\tGT:AC:AF:NC\t0:3:0.0576923076923:A=1,T=49,G=3,\t0:0:0:T=31,\n+phiX174\t1384\t.\tT\tG\t0\t.\tAC=4;AF=0.0512820512821\tGT:AC:AF:NC\t0:4:0.0816326530612:T=45,G=4,\t0:0:0:T=29,G=1,\n+phiX174\t1385\t.\tT\tG\t0\t.\tAC=4;AF=0.0512820512821\tGT:AC:AF:NC\t0:4:0.0816326530612:T=45,G=4,\t0:0:0:C=1,T=29,\n+phiX174\t1391\t.\tA\tC\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:2:0.0408163265306:A=47,C=2,\t0:0:0:A=30,C=1,\n+phiX174\t1393\t.\tC\tA\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:2:0.0425531914894:A=2,C=45,\t0:0:0:C=32,\n+phiX174\t1396\t.\tT\tG\t0\t.\tAC=3;AF=0.04\tGT:AC:AF:NC\t0:3:0.0697674418605:T=40,G=3,\t0:0:0:T=32,\n+phiX174\t1397\t.\tA\tC\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:0:0:A=42,T=1,\t0:2:0.0625:A=30,C=2,\n+phiX174\t1400\t.\tA\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.047619047619:A=40,C=2,G=1,\t0:0:0:A=31,\n+phiX174\t1401\t.\tA\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.047619047619:A=40,C=2,\t0:0:0:A=31,\n+phiX174\t1434\t.\tC\tT\t0\t.\tAC=2;AF=0.0571428571429\tGT:AC:AF:NC\t0:2:0.142857142857:C=12,T=2,\t0:0:0:C=21,\n+phiX174\t1438\t.\tG\tC\t0\t.\tAC=2;AF=0.0526315789474\tGT:AC:AF:NC\t0:0:0:G=15,\t0:2:0.0869565217391:C=2,G=21,\n+phiX174\t1450\t.\tT\tG\t0\t.\tAC=3;AF=0.0789473684211\tGT:AC:AF:NC\t0:3:0.176470588235:A=1,C=1,T=14,G=3,\t0:0:0:T=21,G=1,\n+phiX174\t1459\t.\tT\tG\t0\t.\tAC=3;AF=0.075\tGT:AC:AF:NC\t0:3:0.142857142857:C=1,T=18,G=3,\t0:0:0:T=19,\n+phiX174\t1470\t.\tC\tA\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:0:0:C=29,\t0:2:0.0869565217391:A=2,C=21,\n+phiX174\t1484\t.\tC\tG\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:2:0.0740740740741:A=1,C=25,G=2,\t0:0:0:C=25,\n+phiX174\t1487\t.\tT\tG\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.0689655172414:T=27,G=2,\t0:0:0:T=26,\n+phiX174\t1491\t.\tG\tT\t0\t.\tAC=2;AF=0.037037037037\tGT:AC:AF:NC\t0:0:0:T=1,G=26,\t0:2:0.0714285714286:T=2,G=26,\n+phiX174\t1503\t.\tA\tC\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:0:0:A=20,C=1,\t0:2:0.0833333333333:A=22,C=2,\n+phiX174\t1536\t.\tA\tC\t0\t.\tAC=3;AF=0.0545454545455\tGT:AC:AF:NC\t0:3:0.111111111111:A=24,C=3,\t0:0:0:A=28,C=1,\n+phiX174\t1541\t.\tT\tG\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.0740740740741:T=25,G=2,\t0:0:0:T=28,\n+phiX174\t1553\t.\tA\tG\t0\t.\tAC=2;AF=0.0408163265306\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=1,G=2,\t0:0:0:A=28,\n+phiX174\t1566\t.\tC\tG\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0:0:C=30,T=1,\t0:2:0.0571428571429:C=33,G=2,\n+phiX174\t1572\t.\tT\tG\t0\t.\tAC=2;AF=0.03125\tGT:AC:AF:NC\t0:2:0.0625:T=30,G=2,\t0:0:0:T=32,\n+phiX174\t1574\t.\tG\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0882352941176:C=3,G=31,\t0:0:0:G=34,\n+phiX174\t1575\t.\tA\tC\t0\t.\tAC=2;AF=0.0294117647059\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=33,T=1,\n+phiX174\t1577\t.\tA\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:0:0:A=35,\t0:3:0.0909090909091:A=30,C=3,\n+phiX174\t1581\t.\tT\tG\t0\t.\tAC=2;AF=0.0285714285714\tGT:AC:AF:NC\t0:2:0.0555555555556:C=1,T=34,G=2,\t0:0:0:T=34,G=1,\n+phiX174\t1591\t.\tA\tC\t0\t.\tAC=3;AF=0.037037037037\tGT:AC:AF:NC\t0:3:0.0789473684211:A=35,C=3,\t0:0:0:A=43,C=1,\n+phiX174\t1597\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0606060606061:T=31,G=2,\t0:0:0:C=1,T=45,\n'
b
diff -r 000000000000 -r 38d93ca9c0f0 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Mar 19 14:31:30 2015 -0400
b
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
b
diff -r 000000000000 -r 38d93ca9c0f0 vcfflatten.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfflatten.xml Thu Mar 19 14:31:30 2015 -0400
b
@@ -0,0 +1,30 @@
+<tool id="vcfflatten2" name="VCFflatten:" version="0.0.3">
+  <description>Removes multi-allelic sites by picking the most common alternate</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>vcfflatten "${input1}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="vcfflatten-input1.vcf"/>
+      <output name="out_file1" file="vcfflatten-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Removes multi-allelic sites by picking the most common alternate.  Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype.
+
+----
+
+Vcfflatten @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>