# HG changeset patch
# User veg
# Date 1479319864 18000
# Node ID 7cb6d7eb557dcce38bfabfacd7880cf315908549

Uploaded

diff -r 000000000000 -r 7cb6d7eb557d tn93/.shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93/.shed.yml	Wed Nov 16 13:11:04 2016 -0500
@@ -0,0 +1,10 @@
+name: tn93
+owner: veg
+description: A few handy bioinformatics tools not already within BioPython
+long_description: |
+  Long description goes here.
+remote_repository_url: https://github.com/davebx/bioext-gx/
+homepage_url: https://pypi.python.org/pypi/biopython-extensions/
+type: unrestricted
+categories:
+ - Next Gen Mappers
diff -r 000000000000 -r 7cb6d7eb557d tn93/test-data/tn93-in1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93/test-data/tn93-in1.fa	Wed Nov 16 13:11:04 2016 -0500
@@ -0,0 +1,224 @@
+>B_FR_83_HXB2_ACC_K03455_5
+CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC
+AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA
+GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACCTTC
+>B_US_83_RF_ACC_M17451
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT
+TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA
+AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA
+CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT
+CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC
+GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG
+CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA
+TAATAGGAGCAGAAACTTTC
+>B_US_86_JRFL_ACC_U63632
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA
+AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA
+ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG
+GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>B_US_90_WEAU160_ACC_U21135
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC
+AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA
+AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA
+GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG
+CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>D_CD_83_ELI_ACC_K03454_7
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAAGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCCTTTACCATATCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATGGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGGACA
+AAAATAGAGAAATTAAGAGAACATCTATTGAGGTGGGGATTTACCAGACC
+AGATAAAAAACATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGTCTATAAAACTGCCAGAAAAGGAG
+AGCTGGACTGTCAATGATATACAGAACTTAGTGGAGAGATTAAACTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTTTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAGCA
+ATTAGCAGAGGCAGTGCAAAGAATATCCACAGAAAGCATAGTGATATGGG
+GAAGGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGGCAGAGTATTGGCAAGCCACTTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_83_NDK_ACC_M27323
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATATAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACC
+AGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGC
+AAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGG
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAA
+ACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_84_84ZR085_ACC_U88822
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTA
+AAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTC
+AATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCA
+AAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGC
+AAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+GTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_UG_94_94UG114_ACC_U88824
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAC
+TAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTC
+AGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTA
+GTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCA
+CAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACC
+AGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTA
+GGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGC
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+AAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAA
+ACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGT
+CAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCA
+TAGTAGGAGCAGAAACTTTC
diff -r 000000000000 -r 7cb6d7eb557d tn93/test-data/tn93-out1.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93/test-data/tn93-out1.csv	Wed Nov 16 13:11:04 2016 -0500
@@ -0,0 +1,29 @@
+ID1,ID2,Distance
+B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994
+B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856
+B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797
+B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156
+B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328
+B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097
+B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218
+B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044
+B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908
+B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203
+B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566
+B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011
+B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759
+B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206
+B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066
+B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054
+D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586
+B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146
+D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974
+D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948
+B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619
+B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213
+D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626
+B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988
+D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033
+D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088
diff -r 000000000000 -r 7cb6d7eb557d tn93/tn93.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93/tn93.xml	Wed Nov 16 13:11:04 2016 -0500
@@ -0,0 +1,102 @@
+<?xml version="1.0"?>
+<tool id="tn93" version="1.0.0" name="TN93">
+  <description/>
+  <requirements>
+    <requirement type="package" version="1.0.4">tn93</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:"/>
+  </stdio>
+  <version_command/>
+  <command><![CDATA[
+        tn93 -o "$tn93_distances"
+        #if str($options.advanced) == "advanced":
+          -t $options.threshold -a $options.ambigs -g $options.fraction -f $format
+          -l $options.overlap
+          #if len(str($options.counts_in_name)) > 0:
+            -d $options.counts_in_name
+          #end if
+        #end if
+        "$input_fasta"
+    ]]></command>
+  <inputs>
+    <param name="input_fasta" label="Input FASTA" type="data" format="fasta"/>
+    <param label="Output format" name="format" type="select">
+      <option value="csv">csv</option>
+      <option value="csvn">csvn</option>
+      <option value="hyphy">hyphy</option>
+    </param>
+    <conditional name="options">
+      <param label="Additional options" name="advanced" type="select">
+        <option value="defaults">Use defaults</option>
+        <option value="advanced">Specify additional parameters</option>
+      </param>
+      <when value="defaults"/>
+      <when value="advanced">
+        <param label="THRESHOLD" name="threshold" type="float" value="0.015" default="0.015"/>
+        <param label="AMBIGS" name="ambigs" type="select">
+          <option value="handle">handle</option>
+          <option value="resolve">resolve</option>
+          <option value="average">average</option>
+          <option value="skip">skip</option>
+          <option value="gapmm">gapmm</option>
+        </param>
+        <param label="FRACTION" name="fraction" type="float" value="1.0" default="1.0"/>
+        <param label="OVERLAP" name="overlap" type="integer" value="100" default="100"/>
+        <param label="COUNTS_IN_NAME" name="counts_in_name" type="text"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="csv" name="tn93_distances">
+      <change_format>
+        <when input="format" value="csvn" format="csvn"/>
+        <when input="format" value="hyphy" format="hyphy"/>
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <!--       <param name="history_reference" value="tn93-in-ref-1.fa"/> -->
+      <param name="input_fasta" value="tn93-in1.fa"/>
+      <param name="advanced" value="advanced"/>
+      <param name="threshold" value="0.35"/>
+      <output file="tn93-out1.csv" ftype="csv" name="tn93_distances" lines_diff="32"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+		optional arguments:
+			-h, --help               show this help message and exit
+			-o OUTPUT                direct the output to a file named OUTPUT (default=stdout)
+			-t THRESHOLD             only report (count) distances below this threshold (>=0, default=0.015)
+			-a AMBIGS                handle ambigous nucleotides using one of the following strategies (default=resolve)
+															 resolve: resolve ambiguities to minimize distance (e.g.R matches A);
+															 average: average ambiguities (e.g.R-A is 0.5 A-A and 0.5 G-A);
+															 skip: do not include sites with ambiguous nucleotides in distance calculations;
+															 gapmm: a gap ('-') matched to anything other than another gap is like matching an N (4-fold ambig) to it;
+															 a string (e.g. RY): any ambiguity in the list is RESOLVED; any ambiguitiy NOT in the list is averaged (LIST-NOT LIST will also be averaged);
+			-g FRACTION              in combination with AMBIGS, works to limit (for resolve and string options to AMBIG)
+															 the maximum tolerated FRACTION of ambiguous characters; sequences whose pairwise comparisons
+															 include no more than FRACTION [0,1] of sites with resolvable ambiguities will be resolved
+															 while all others will be AVERAGED (default = 1.0)
+			-f FORMAT                controls the format of the output unless -c is set (default=csv)
+															 csv: seqname1, seqname2, distance;
+															 csvn: 1, 2, distance;
+															 hyphy: {{d11,d12,..,d1n}...{dn1,dn2,...,dnn}}, where distances above THRESHOLD are set to 100;
+			-l OVERLAP               only process pairs of sequences that overlap over at least OVERLAP nucleotides (an integer >0, default=100):
+			-d COUNTS_IN_NAME        if sequence name is of the form 'somethingCOUNTS_IN_NAMEinteger' then treat the integer as a copy number
+															 when computing distance histograms (a character, default=':'):
+			-s SECOND_FASTA          if specified, read another FASTA file from SECOND_FASTA and perform pairwise comparison BETWEEN the files (default=NULL)
+			-b                       bootstrap alignment columns before computing distances (default = false)
+															 when -s is supplied, permutes the assigment of sequences to files
+															 interacts with -r option
+			-r                       if -b is specified AND -s is supplied, using -r will bootstrap across sites
+															 instead of allocating sequences to 'compartments' randomly
+			-c                       only count the pairs below a threshold, do not write out all the pairs
+			-m                       compute inter- and intra-population means suitable for FST caclulations
+															 only applied when -s is used to provide a second file
+			-u PROBABILITY           subsample sequences with specified probability (a value between 0 and 1, default = 1.0)
+			-q                       do not report progress updates and other diagnostics to stderr
+			FASTA                    read sequences to compare from this file (default=stdin)
+]]></help>
+</tool>