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Changeset 0:d7d4d88ae84d (2015-03-19)

Next changeset 1:046b3db333bd (2015-11-11)

Commit message:
Uploaded

added:
macros.xml
test-data/vcfcheck-test1.vcf
test-data/vcflib-phix.vcf
test-data/vcflib-test-genome-phix.fa
tool-data/fasta_indexes.loc.sample
tool-data/tool_data_table_conf.xml.sample
tool_dependencies.xml
vcfcheck.xml

diff -r 000000000000 -r d7d4d88ae84d macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Mar 19 13:34:33 2015 -0400

@@ -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>

diff -r 000000000000 -r d7d4d88ae84d test-data/vcfcheck-test1.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfcheck-test1.vcf Thu Mar 19 13:34:33 2015 -0400

b'@@ -0,0 +1,219 @@\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'\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0810810810811:A=34,G=3,\t0:0:0:A=31,\n+phiX174\t1775\t.\tG\tA\t0\t.\tAC=2;AF=0.030303030303\tGT:AC:AF:NC\t0:2:0.0571428571429:A=2,G=33,\t0:0:0:G=31,\n+phiX174\t1776\t.\tG\tT\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0540540540541:T=2,G=35,\t0:0:0:G=32,\n+phiX174\t1778\t.\tC\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0526315789474:C=36,G=2,\t0:0:0:C=31,\n+phiX174\t1779\t.\tA\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.075:A=37,C=3,\t0:0:0:A=28,\n+phiX174\t1781\t.\tT\tG\t0\t.\tAC=5;AF=0.0714285714286\tGT:AC:AF:NC\t0:2:0.0487804878049:C=1,T=39,G=2,\t0:3:0.103448275862:T=26,G=3,\n+phiX174\t1782\t.\tT\tG\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.075:T=37,G=3,\t0:0:0:A=1,T=28,\n+phiX174\t1783\t.\tT\tC\t0\t.\tAC=2;AF=0.0298507462687\tGT:AC:AF:NC\t0:2:0.0512820512821:C=2,T=37,\t0:0:0:T=28,G=1,\n+phiX174\t1788\t.\tG\tT\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:0:0:A=1,T=1,G=29,\t0:2:0.0689655172414:T=2,G=27,\n+phiX174\t1792\t.\tT\tG\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:2:0.0606060606061:T=31,G=2,\t0:0:0:T=25,G=1,\n+phiX174\t1802\t.\tA\tC\t0\t.\tAC=2;AF=0.030303030303\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=31,C=1,\n+phiX174\t1804\t.\tC\tT\t0\t.\tAC=2;AF=0.0294117647059\tGT:AC:AF:NC\t0:2:0.0588235294118:A=1,C=32,T=2,\t0:0:0:C=34,\n+phiX174\t1805\t.\tT\tG\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0857142857143:T=32,G=3,\t0:0:0:T=33,G=1,\n+phiX174\t1806\t.\tA\tC\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=34,G=1,\n+phiX174\t1824\t.\tG\tC\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0714285714286:C=2,T=1,G=26,\t0:0:0:G=43,\n+phiX174\t1825\t.\tT\tG\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0689655172414:T=27,G=2,\t0:0:0:T=42,G=1,\n+phiX174\t1833\t.\tT\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:0:0:A=1,T=24,\t0:2:0.0444444444444:T=43,G=2,\n+phiX174\t1843\t.\tT\tG\t0\t.\tAC=2;AF=0.031746031746\tGT:AC:AF:NC\t0:2:0.08:A=1,T=23,G=2,\t0:0:0:T=38,\n+phiX174\t1847\t.\tA\tC\t0\t.\tAC=2;AF=0.0333333333333\tGT:AC:AF:NC\t0:2:0.0833333333333:A=22,C=2,T=1,G=1,\t0:0:0:A=36,\n+phiX174\t1854\t.\tT\tG\t0\t.\tAC=2;AF=0.0298507462687\tGT:AC:AF:NC\t0:0:0:T=26,\t0:2:0.0487804878049:T=39,G=2,\n+phiX174\t1860\t.\tT\tG\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:0:0:A=1,T=20,\t0:2:0.0606060606061:T=31,G=2,\n+phiX174\t1863\t.\tC\tG\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=17,G=2,\t0:0:0:C=33,\n+phiX174\t1866\t.\tT\tG\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:0:0:T=19,G=1,\t0:2:0.0645161290323:T=29,G=2,\n+phiX174\t1875\t.\tT\tA\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:2:0.0952380952381:A=2,T=19,\t0:0:0:T=32,G=1,\n+phiX174\t1876\t.\tT\tG\t0\t.\tAC=3;AF=0.0588235294118\tGT:AC:AF:NC\t0:3:0.157894736842:C=1,T=16,G=3,\t0:0:0:T=32,G=1,\n+phiX174\t1882\t.\tT\tG\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:2:0.105263157895:T=17,G=2,\t0:0:0:T=34,\n+phiX174\t1889\t.\tA\tC\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:2:0.0869565217391:A=21,C=2,\t0:0:0:A=27,\n+phiX174\t1913\t.\tG\tC\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:0:0:G=27,\t0:2:0.0869565217391:C=2,G=21,\n+phiX174\t1915\t.\tT\tG\t0\t.\tAC=2;AF=0.0425531914894\tGT:AC:AF:NC\t0:0:0:A=1,T=24,\t0:2:0.0869565217391:T=21,G=2,\n+phiX174\t1917\t.\tA\tT\t0\t.\tAC=2;AF=0.0444444444444\tGT:AC:AF:NC\t0:2,0:0.0833333333333,0:A=22,T=2,G=1,\t0:0,0:0,0:A=21,G=1,\n+phiX174\t1930\t.\tT\tA\t0\t.\tAC=2;AF=0.0526315789474\tGT:AC:AF:NC\t0:2:0.0909090909091:A=2,T=20,\t0:0:0:T=16,\n+phiX174\t1934\t.\tA\tC\t0\t.\tAC=2;AF=0.0512820512821\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=2,T=1,\t0:0:0:A=18,C=1,\n+phiX174\t1940\t.\tA\tC\t0\t.\tAC=2;AF=0.046511627907\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=2,\t0:0:0:A=22,C=1,\n+phiX174\t1942\t.\tT\tG\t0\t.\tAC=2;AF=0.047619047619\tGT:AC:AF:NC\t0:0:0:T=19,\t0:2:0.0869565217391:T=21,G=2,\n+phiX174\t1945\t.\tT\tG\t0\t.\tAC=3;AF=0.0769230769231\tGT:AC:AF:NC\t0:0:0:T=15,G=1,\t0:3:0.125:T=21,G=3,\n+phiX174\t1954\t.\tT\tC\t0\t.\tAC=2;AF=0.0625\tGT:AC:AF:NC\t0:0,0:0,0:T=12,G=1,\t0:0,2:0,0.1:C=2,T=18,G=1,\n+phiX174\t1959\t.\tT\tG\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:2:0.153846153846:T=11,G=2,\t0:0:0:T=23,\n+phiX174\t1994\t.\tA\tC\t0\t.\tAC=2;AF=0.0512820512821\tGT:AC:AF:NC\t0:2:0.153846153846:A=11,C=2,\t0:0:0:A=26,\n+phiX174\t1998\t.\tA\tG\t0\t.\tAC=2;AF=0.05\tGT:AC:AF:NC\t0:2:0.142857142857:A=12,G=2,\t0:0:0:A=26,\n'

diff -r 000000000000 -r d7d4d88ae84d test-data/vcflib-phix.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-phix.vcf Thu Mar 19 13:34:33 2015 -0400

diff -r 000000000000 -r d7d4d88ae84d test-data/vcflib-test-genome-phix.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-test-genome-phix.fa Thu Mar 19 13:34:33 2015 -0400

@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA

diff -r 000000000000 -r d7d4d88ae84d tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Thu Mar 19 13:34:33 2015 -0400

@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id> <dbkey> <display_name> <file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa

diff -r 000000000000 -r d7d4d88ae84d tool-data/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample Thu Mar 19 13:34:33 2015 -0400

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

diff -r 000000000000 -r d7d4d88ae84d tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Mar 19 13:34:33 2015 -0400

@@ -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>

diff -r 000000000000 -r d7d4d88ae84d vcfcheck.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfcheck.xml Thu Mar 19 13:34:33 2015 -0400

@@ -0,0 +1,74 @@
+<tool id="vcfcheck" name="VCFcheck:" version="0.0.3">
+  <description>Verify that the reference allele matches the reference genome</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <command>
+    #set $reference_fasta_filename = "localref.fa"
+    #if str( $reference_source.reference_source_selector ) == "history":
+       ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
+    #else:
+       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if
+  vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
+  <inputs>
+    <conditional name="reference_source">
+       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+         <option value="cached">Locally cached</option>
+         <option value="history">History</option>
+       </param>
+       <when value="cached">
+         <param name="ref_file" type="select" label="Select reference genome">
+           <options from_data_table="fasta_indexes">
+             
+           </options>
+    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+         </param>
+ <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
+    
+ </param>
+       </when>
+       <when value="history"> 
+         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+ <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
+       </when>
+     </conditional>
+     <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
+       <option value="-x">Exculde failures (-x option)</option>
+       <option value="-k">Keep failures (-k option)</option>
+     </param>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <stdio>
+    <regex match="index file" source="stderr" level="warning"/>
+  </stdio>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="failure_selection" value="-x" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <output name="out_file1" file="vcfcheck-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Verifies that the VCF REF field matches the reference as described.
+
+The options are::
+
+    -x, --exclude-failures If a record fails, don't print it.  Otherwise do.
+    -k, --keep-failures    Print if the record fails, otherwise not.
+
+----
+
+Vcfcheck @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>