Repository 'vcfprimers'
hg clone https://eddie.galaxyproject.org/repos/devteam/vcfprimers

Changeset 0:15ec0bdaf4dd (2015-11-09)
Next changeset 1:15de96f45d4d (2015-11-12)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfprimers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
added:
macros.xml
test-data/vcflib-phix.vcf
test-data/vcflib-test-genome-phix.fa
test-data/vcfprimers-test1.fasta
tool_dependencies.xml
vcfprimers.xml
b
diff -r 000000000000 -r 15ec0bdaf4dd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Nov 09 12:33:41 2015 -0500
b
@@ -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>
b
diff -r 000000000000 -r 15ec0bdaf4dd test-data/vcflib-phix.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-phix.vcf Mon Nov 09 12:33:41 2015 -0500
b
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'
b
diff -r 000000000000 -r 15ec0bdaf4dd 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 Mon Nov 09 12:33:41 2015 -0500
b
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
b
diff -r 000000000000 -r 15ec0bdaf4dd test-data/vcfprimers-test1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfprimers-test1.fasta Mon Nov 09 12:33:41 2015 -0500
b
b'@@ -0,0 +1,828 @@\n+>phiX174_1015_LEFT\n+ATTCA\n+>phiX174_1015_RIGHT\n+ACTGG\n+>phiX174_1016_LEFT\n+TTCAA\n+>phiX174_1016_RIGHT\n+CTGGC\n+>phiX174_1038_LEFT\n+GCCGC\n+>phiX174_1038_RIGHT\n+TGACC\n+>phiX174_1045_LEFT\n+GACCT\n+>phiX174_1045_RIGHT\n+TCCCA\n+>phiX174_1048_LEFT\n+CTTTC\n+>phiX174_1048_RIGHT\n+CATCT\n+>phiX174_1050_LEFT\n+TTCCC\n+>phiX174_1050_RIGHT\n+TCTTG\n+>phiX174_1051_LEFT\n+TCCCA\n+>phiX174_1051_RIGHT\n+CTTGG\n+>phiX174_1054_LEFT\n+CATCT\n+>phiX174_1054_RIGHT\n+GGCTT\n+>phiX174_1076_LEFT\n+AGATT\n+>phiX174_1076_RIGHT\n+GTCGT\n+>phiX174_1080_LEFT\n+TGGTC\n+>phiX174_1080_RIGHT\n+TCTTA\n+>phiX174_1092_LEFT\n+TACCA\n+>phiX174_1092_RIGHT\n+TTCAA\n+>phiX174_1093_LEFT\n+ACCAT\n+>phiX174_1093_RIGHT\n+TCAAC\n+>phiX174_1102_LEFT\n+ACTAC\n+>phiX174_1102_RIGHT\n+CCGGT\n+>phiX174_1107_LEFT\n+TCCGG\n+>phiX174_1107_RIGHT\n+TATCG\n+>phiX174_1110_LEFT\n+GGTTA\n+>phiX174_1110_RIGHT\n+CGCTG\n+>phiX174_1121_LEFT\n+GCGAC\n+>phiX174_1121_RIGHT\n+CCTTC\n+>phiX174_1124_LEFT\n+ACTCC\n+>phiX174_1124_RIGHT\n+TCGAG\n+>phiX174_1125_LEFT\n+CTCCT\n+>phiX174_1125_RIGHT\n+CGAGA\n+>phiX174_1131_LEFT\n+CGAGA\n+>phiX174_1131_RIGHT\n+GGACG\n+>phiX174_1141_LEFT\n+GCCGT\n+>phiX174_1141_RIGHT\n+GGCGC\n+>phiX174_1145_LEFT\n+TTGGC\n+>phiX174_1145_RIGHT\n+CTCTC\n+>phiX174_1147_LEFT\n+GGCGC\n+>phiX174_1147_RIGHT\n+CTCCG\n+>phiX174_1149_LEFT\n+CGCTC\n+>phiX174_1149_RIGHT\n+CCGTC\n+>phiX174_1156_LEFT\n+CGTCT\n+>phiX174_1156_RIGHT\n+TCTCC\n+>phiX174_1159_LEFT\n+CTTTC\n+>phiX174_1159_RIGHT\n+CCATT\n+>phiX174_1164_LEFT\n+TCCAT\n+>phiX174_1164_RIGHT\n+GCGTC\n+>phiX174_1168_LEFT\n+TTGCG\n+>phiX174_1168_RIGHT\n+CGTGG\n+>phiX174_1171_LEFT\n+CGTCG\n+>phiX174_1171_RIGHT\n+GGCCT\n+>phiX174_1174_LEFT\n+CGTGG\n+>phiX174_1174_RIGHT\n+CTTGC\n+>phiX174_1178_LEFT\n+GCCTT\n+>phiX174_1178_RIGHT\n+CTATT\n+>phiX174_1187_LEFT\n+TTGAC\n+>phiX174_1187_RIGHT\n+CTACT\n+>phiX174_1189_LEFT\n+GACTC\n+>phiX174_1189_RIGHT\n+ACTGT\n+>phiX174_1200_LEFT\n+AGACA\n+>phiX174_1200_RIGHT\n+TTTTA\n+>phiX174_1202_LEFT\n+ACATT\n+>phiX174_1202_RIGHT\n+TTACT\n+>phiX174_1205_LEFT\n+TTTTT\n+>phiX174_1205_RIGHT\n+CTTTT\n+>phiX174_1207_LEFT\n+TTTAC\n+>phiX174_1207_RIGHT\n+TTTTA\n+>phiX174_1214_LEFT\n+TTTAT\n+>phiX174_1214_RIGHT\n+TCCCT\n+>phiX174_1216_LEFT\n+TATGT\n+>phiX174_1216_RIGHT\n+CCTCA\n+>phiX174_1217_LEFT\n+ATGTC\n+>phiX174_1217_RIGHT\n+CTCAT\n+>phiX174_1219_LEFT\n+GTCCC\n+>phiX174_1219_RIGHT\n+CATCG\n+>phiX174_1223_LEFT\n+CTCAT\n+>phiX174_1223_RIGHT\n+GTCAC\n+>phiX174_1227_LEFT\n+TCGTC\n+>phiX174_1227_RIGHT\n+CGTTT\n+>phiX174_1232_LEFT\n+ACGTT\n+>phiX174_1232_RIGHT\n+ATGGT\n+>phiX174_1236_LEFT\n+TTATG\n+>phiX174_1236_RIGHT\n+TGAAC\n+>phiX174_1237_LEFT\n+TATGG\n+>phiX174_1237_RIGHT\n+GAACA\n+>phiX174_1240_LEFT\n+GGTGA\n+>phiX174_1240_RIGHT\n+CAGTG\n+>phiX174_1245_LEFT\n+ACAGT\n+>phiX174_1245_RIGHT\n+GATTA\n+>phiX174_1247_LEFT\n+AGTGG\n+>phiX174_1247_RIGHT\n+TTAAG\n+>phiX174_1250_LEFT\n+GGATT\n+>phiX174_1250_RIGHT\n+AGTTC\n+>phiX174_1251_LEFT\n+GATTA\n+>phiX174_1251_RIGHT\n+GTTCA\n+>phiX174_1253_LEFT\n+TTAAG\n+>phiX174_1253_RIGHT\n+TCATG\n+>phiX174_1257_LEFT\n+GTTCA\n+>phiX174_1257_RIGHT\n+GAAGG\n+>phiX174_1259_LEFT\n+TCATG\n+>phiX174_1259_RIGHT\n+AGGAT\n+>phiX174_1274_LEFT\n+TTAAT\n+>phiX174_1274_RIGHT\n+CCACT\n+>phiX174_1277_LEFT\n+ATGCC\n+>phiX174_1277_RIGHT\n+CTCCT\n+>phiX174_1279_LEFT\n+GCCAC\n+>phiX174_1279_RIGHT\n+CCTCT\n+>phiX174_1284_LEFT\n+TCCTC\n+>phiX174_1284_RIGHT\n+CCCGA\n+>phiX174_1289_LEFT\n+TCCCG\n+>phiX174_1289_RIGHT\n+CTGTT\n+>phiX174_1296_LEFT\n+TGTTA\n+>phiX174_1296_RIGHT\n+CACTA\n+>phiX174_1298_LEFT\n+TTAAC\n+>phiX174_1298_RIGHT\n+CTACT\n+>phiX174_1306_LEFT\n+ACTGG\n+>phiX174_1306_RIGHT\n+TATAT\n+>phiX174_1307_LEFT\n+CTGGT\n+>phiX174_1307_RIGHT\n+ATATT\n+>phiX174_1314_LEFT\n+TATTG\n+>phiX174_1314_RIGHT\n+CCATG\n+>phiX174_1317_LEFT\n+TGACC\n+>phiX174_1317_RIGHT\n+TGCCG\n+>phiX174_1320_LEFT\n+CCATG\n+>phiX174_1320_RIGHT\n+CGCTT\n+>phiX174_1322_LEFT\n+ATGCC\n+>phiX174_1322_RIGHT\n+CTTTT\n+>phiX174_1323_LEFT\n+TGCCG\n+>phiX174_1323_RIGHT\n+TTTTC\n+>phiX174_1329_LEFT\n+TTTTC\n+>phiX174_1329_RIGHT\n+TGGCA\n+>phiX174_1335_LEFT\n+TGGCA\n+>phiX174_1335_RIGHT\n+GATTA\n+>phiX174_1338_LEFT\n+CACGA\n+>phiX174_1338_RIGHT\n+TAACC\n+>phiX174_1345_LEFT\n+AACCC\n+>phiX174_1345_RIGHT\n+GATAC\n+>phiX174_1347_LEFT\n+CCCTG\n+>phiX174_1347_RIGHT\n+TACCA\n+>phiX174_1348_LEFT\n+'..b'EFT\n+TTTGG\n+>phiX174_1672_RIGHT\n+GGTAA\n+>phiX174_1673_LEFT\n+TTGGA\n+>phiX174_1673_RIGHT\n+GTAAA\n+>phiX174_1674_LEFT\n+TGGAG\n+>phiX174_1674_RIGHT\n+TAAAA\n+>phiX174_1677_LEFT\n+AGGTA\n+>phiX174_1677_RIGHT\n+AACCT\n+>phiX174_1678_LEFT\n+GGTAA\n+>phiX174_1678_RIGHT\n+ACCTC\n+>phiX174_1682_LEFT\n+AAACC\n+>phiX174_1682_RIGHT\n+CTTAT\n+>phiX174_1685_LEFT\n+CCTCT\n+>phiX174_1685_RIGHT\n+ATGAC\n+>phiX174_1686_LEFT\n+CTCTT\n+>phiX174_1686_RIGHT\n+TGACG\n+>phiX174_1687_LEFT\n+TCTTA\n+>phiX174_1687_RIGHT\n+GACGC\n+>phiX174_1688_LEFT\n+CTTAT\n+>phiX174_1688_RIGHT\n+ACGCT\n+>phiX174_1689_LEFT\n+TTATG\n+>phiX174_1689_RIGHT\n+CGCTG\n+>phiX174_1691_LEFT\n+ATGAC\n+>phiX174_1691_RIGHT\n+CTGAC\n+>phiX174_1693_LEFT\n+GACGC\n+>phiX174_1693_RIGHT\n+GACAA\n+>phiX174_1695_LEFT\n+CGCTG\n+>phiX174_1695_RIGHT\n+CAACC\n+>phiX174_1702_LEFT\n+AACCG\n+>phiX174_1702_RIGHT\n+CCTTT\n+>phiX174_1707_LEFT\n+TCCTT\n+>phiX174_1707_RIGHT\n+ACTTG\n+>phiX174_1708_LEFT\n+CCTTT\n+>phiX174_1708_RIGHT\n+CTTGT\n+>phiX174_1710_LEFT\n+TTTAC\n+>phiX174_1710_RIGHT\n+TGTCA\n+>phiX174_1723_LEFT\n+CGCTC\n+>phiX174_1723_RIGHT\n+AATCT\n+>phiX174_1724_LEFT\n+GCTCT\n+>phiX174_1724_RIGHT\n+ATCTC\n+>phiX174_1725_LEFT\n+CTCTA\n+>phiX174_1725_RIGHT\n+TCTCT\n+>phiX174_1726_LEFT\n+TCTAA\n+>phiX174_1726_RIGHT\n+CTCTG\n+>phiX174_1730_LEFT\n+ATCTC\n+>phiX174_1730_RIGHT\n+GGGCA\n+>phiX174_1739_LEFT\n+CATCT\n+>phiX174_1739_RIGHT\n+GCTAT\n+>phiX174_1746_LEFT\n+CTATG\n+>phiX174_1746_RIGHT\n+TGTTG\n+>phiX174_1749_LEFT\n+TGATG\n+>phiX174_1749_RIGHT\n+TGATG\n+>phiX174_1755_LEFT\n+TGATG\n+>phiX174_1755_RIGHT\n+AACTG\n+>phiX174_1756_LEFT\n+GATGG\n+>phiX174_1756_RIGHT\n+ACTGA\n+>phiX174_1761_LEFT\n+AACTG\n+>phiX174_1761_RIGHT\n+CCAAA\n+>phiX174_1764_LEFT\n+TGACC\n+>phiX174_1764_RIGHT\n+AACGT\n+>phiX174_1766_LEFT\n+ACCAA\n+>phiX174_1766_RIGHT\n+CGTCG\n+>phiX174_1769_LEFT\n+AAACG\n+>phiX174_1769_RIGHT\n+CGTTA\n+>phiX174_1771_LEFT\n+ACGTC\n+>phiX174_1771_RIGHT\n+TTAGG\n+>phiX174_1772_LEFT\n+CGTCG\n+>phiX174_1772_RIGHT\n+TAGGC\n+>phiX174_1774_LEFT\n+TCGTT\n+>phiX174_1774_RIGHT\n+GGCCA\n+>phiX174_1775_LEFT\n+CGTTA\n+>phiX174_1775_RIGHT\n+GCCAG\n+>phiX174_1776_LEFT\n+GTTAG\n+>phiX174_1776_RIGHT\n+CCAGT\n+>phiX174_1778_LEFT\n+TAGGC\n+>phiX174_1778_RIGHT\n+AGTTT\n+>phiX174_1779_LEFT\n+AGGCC\n+>phiX174_1779_RIGHT\n+GTTTT\n+>phiX174_1781_LEFT\n+GCCAG\n+>phiX174_1781_RIGHT\n+TTTCT\n+>phiX174_1782_LEFT\n+CCAGT\n+>phiX174_1782_RIGHT\n+TTCTG\n+>phiX174_1783_LEFT\n+CAGTT\n+>phiX174_1783_RIGHT\n+TCTGG\n+>phiX174_1788_LEFT\n+TTCTG\n+>phiX174_1788_RIGHT\n+TCGTG\n+>phiX174_1792_LEFT\n+GGTCG\n+>phiX174_1792_RIGHT\n+GTTCA\n+>phiX174_1802_LEFT\n+AACAG\n+>phiX174_1802_RIGHT\n+CCTAT\n+>phiX174_1804_LEFT\n+CAGAC\n+>phiX174_1804_RIGHT\n+TATAA\n+>phiX174_1805_LEFT\n+AGACC\n+>phiX174_1805_RIGHT\n+ATAAA\n+>phiX174_1806_LEFT\n+GACCT\n+>phiX174_1806_RIGHT\n+TAAAC\n+>phiX174_1824_LEFT\n+GCCGC\n+>phiX174_1824_RIGHT\n+TTTCT\n+>phiX174_1825_LEFT\n+CCGCG\n+>phiX174_1825_RIGHT\n+TTCTT\n+>phiX174_1833_LEFT\n+CTTTG\n+>phiX174_1833_RIGHT\n+TCCTG\n+>phiX174_1843_LEFT\n+GAGCA\n+>phiX174_1843_RIGHT\n+GGCAC\n+>phiX174_1847_LEFT\n+ATGGC\n+>phiX174_1847_RIGHT\n+CTATG\n+>phiX174_1854_LEFT\n+TATGT\n+>phiX174_1854_RIGHT\n+TACTC\n+>phiX174_1860_LEFT\n+TACTC\n+>phiX174_1860_RIGHT\n+TGCGC\n+>phiX174_1863_LEFT\n+TCTTG\n+>phiX174_1863_RIGHT\n+GCTTG\n+>phiX174_1866_LEFT\n+TGCGC\n+>phiX174_1866_RIGHT\n+TGTTC\n+>phiX174_1875_LEFT\n+TCGTT\n+>phiX174_1875_RIGHT\n+TCCGC\n+>phiX174_1876_LEFT\n+CGTTT\n+>phiX174_1876_RIGHT\n+CCGCC\n+>phiX174_1882_LEFT\n+CCGCC\n+>phiX174_1882_RIGHT\n+ACTGC\n+>phiX174_1889_LEFT\n+CTGCG\n+>phiX174_1889_RIGHT\n+CTAAA\n+>phiX174_1913_LEFT\n+TTAAC\n+>phiX174_1913_RIGHT\n+CTAAA\n+>phiX174_1915_LEFT\n+AACGC\n+>phiX174_1915_RIGHT\n+AAAGG\n+>phiX174_1917_LEFT\n+CGCTA\n+>phiX174_1917_RIGHT\n+AGGTG\n+>phiX174_1930_LEFT\n+TTGAC\n+>phiX174_1930_RIGHT\n+TATAC\n+>phiX174_1934_LEFT\n+CTTAT\n+>phiX174_1934_RIGHT\n+CCGAT\n+>phiX174_1940_LEFT\n+CCGAT\n+>phiX174_1940_RIGHT\n+TTGCT\n+>phiX174_1942_LEFT\n+GATAT\n+>phiX174_1942_RIGHT\n+GCTGG\n+>phiX174_1945_LEFT\n+ATTGC\n+>phiX174_1945_RIGHT\n+GGCGA\n+>phiX174_1954_LEFT\n+GACCC\n+>phiX174_1954_RIGHT\n+GTTTT\n+>phiX174_1959_LEFT\n+TGTTT\n+>phiX174_1959_RIGHT\n+GTATG\n+>phiX174_1994_LEFT\n+CTATG\n+>phiX174_1994_RIGHT\n+AGGAT\n+>phiX174_1998_LEFT\n+GAAGG\n+>phiX174_1998_RIGHT\n+TGTTT\n'
b
diff -r 000000000000 -r 15ec0bdaf4dd tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Nov 09 12:33:41 2015 -0500
b
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="3ac0905f7b7c" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
b
diff -r 000000000000 -r 15ec0bdaf4dd vcfprimers.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfprimers.xml Mon Nov 09 12:33:41 2015 -0500
b
@@ -0,0 +1,67 @@
+<tool id="vcfprimers" name="VCFprimers:" version="0.0.3">
+  <description>Extract flanking sequences for each VCF record</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></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}" &amp;&amp;
+    #else:
+       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if    
+   vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}"</command>
+  <inputs>
+<param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" />
+    <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>
+       </when>
+       <when value="history"> <!-- FIX ME!!!! -->
+         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+       </when>
+     </conditional>
+     <param name="primer_length" type="integer" value="20" label="The length of the primer sequences on each side of the variant" help="default = 20 bp" />
+  </inputs>
+  <outputs>
+    <data format="fasta" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <param name="primer_length" value="5" />
+      <output name="out_file1" file="vcfprimers-test1.fasta"/>
+    </test>
+    </tests>
+  <help>
+
+For each VCF record, extract the flanking sequences, and write them as FASTA
+records suitable for alignment.  This tool is intended for use in designing validation
+experiments.  Primers extracted which would flank all of the alleles at multi-allelic
+sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.
+The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
+for example::
+
+ >20_233255_LEFT
+ CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA
+ >20_233255_RIGHT
+ ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA
+
+----
+
+Vcfprimers @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>