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changeset 5:ee4a11ebe451 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 1da5a3f152e115430b04ab532541a220a8e0adba
author jdv
date Fri, 01 Dec 2017 22:13:14 -0500
parents bdd6c1ab07c5
children 36cc4ae4160e
files nanopolish_variants.xml test-data/variants.bam test-data/variants.in.fast5.tar.bz2 test-data/variants.out.fa test-data/variants.reads.fa test-data/variants.ref.fa
diffstat 6 files changed, 146 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/nanopolish_variants.xml	Fri Dec 01 21:22:01 2017 -0500
+++ b/nanopolish_variants.xml	Fri Dec 01 22:13:14 2017 -0500
@@ -69,7 +69,14 @@
     <!-- ***************************************************************** -->
 
     <tests>
-        <!-- TODO -->
+        <test>
+            <param name="input_reads" value="variants.reads.fa" ftype="fasta" />
+            <param name="input_fast5" value="variants.in.fast5.tar.bz2" ftype="fast5.tar.bz2" />
+            <param name="input_bam"   value="variants.bam" ftype="bam" />
+            <param name="input_ref"   value="variants.ref.fa" ftype="fasta" />
+            <param name="fix_homopolymers" value="True"/>
+            <output name="out_consensus" file="variants.out.fa" compare="diff" />
+        </test>
     </tests>
 
     <!-- ***************************************************************** -->
Binary file test-data/variants.bam has changed
Binary file test-data/variants.in.fast5.tar.bz2 has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/variants.out.fa	Fri Dec 01 22:13:14 2017 -0500
@@ -0,0 +1,2 @@
+>cluster_0:0-783
+TCATTAACAAATGCTGCATCTTCCCTACTGCTACTGATAGTTGTGATAATCCGTCGGTGACTTCATGCACAGCTTCATTGGTTGCAGCAATGCTCTCCTTAAGCCGGAGGATGTTGGCAGCATTCTGGTTGGCCTGTATTAGGGCCGCAGCTGCTGTTATCTGTGCCGCTGTTGCAACCCCAAGAGCTACACTGCCAATAACGGCACCTATAAAGCGCTTTTGTCTCCTTCCTCAGACGTGGACACAGACCCTTGGATCTTGCGGATGGAATCGCCAAGAGGAGTGAGCAAAGTAGTCAGTGTTCTGTTATATGCCTCTAATGGGGCTTTTGCACACGCCTCCTTATCCTTGGGCATATTCGGGAGCAATTTGACTATGATTGACCCTGTCTGAGACGAGGTGTATACATTGACTGCCTTATCTCCTGTCACTACAATTCCTGCAGCTGCANGAGGCCTGCCGTCAAGGGAGCTTGTCAGACGGATACAGCTCAATATCAGCATAATCCGAGTTATCAGCATCNGAAGTGCTGGGATCCTGGTGAAGGTTTGGAGCCCATATTGCGTCCTGGATGAGCTGGTCGGGATCCAGACCCTTCTACCCGTGTGTTTTTCTAATTTGCTAAACAGGTGAACTAACTATAAGCAGTTGAGATGGATCATTATCTGGTGTCATGTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGGATGCAACTTATTTTCTGAAAGGATTGTATTTGGCAATGGTGTGTCTCTTCTCCAGCTTAGTAGAGGTAACCTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/variants.reads.fa	Fri Dec 01 22:13:14 2017 -0500
@@ -0,0 +1,121 @@
+>88bad4e9-c28f-4b9c-8011-6b07bace6d29
+ACGGTATTGCTTCGTTCAGTTACGTATTGCTGGTGCTGTTGCGTCCTGTACGAGAACTCA
+TTTAACCTACTTGCCTGTCGCTCTATCTTCTCATTAACAACTGCTGCATCTTCCCAACTA
+CTGATGATTTGTGATAATCGTCAGTGACTTCATGCACAACTTCATTGAGTTGCAACAATG
+CTCTCCTTAAACCGGAGGATGTTGGCAGCATTCTGGATGGCCAGCCTGTATTAGGGCCGC
+AGCTGCTGTTATCTGTGCCACTGTTGCAACCCCAGAGCTACACTGCCAATAACAGCTATA
+AAGCGCTTTTGTCTCCTTCACTCCCAGACGGACACAGACCCTTGGATCTTGCGGATGGAA
+TCGCCAAGAAGGAGTGAAGAAGTAGTCAGTGGATGTTGCTTAGCCTCTAATGGGGCTTTT
+ACACGCCTCTTGCTTAGTCGGAGCAATTTGACTATGATTGACCTGTCTGAGACAGATGTA
+TACATTGACTGCCTTATCTCCCTGTCACTGTTCCTGCAGCTGCAAGGCCTGCCGTCAAGG
+GAGCTTGTCAGACGGATACATCTCCAATATATCAGCATAATCGAGTTATCAGCATCAAGA
+ATTCTTTGGGATCCTGTGAAAGGTTTGGAGCCCATATTGCGTCCTGGATGAGCTGGTCAG
+ACCCTTCTACCGATGTTTTTCTAATTTGCTAAACAGACACAACTATAAGCGGATGGATCG
+TATCTGGTGTCGCATGTGTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGGATGCAA
+CTTATTTTCTGTGAAGGATTGTGTACAACTTGTGGTATTGTCTCTTCTCCAACGGTGGAG
+TACTCATATCAGCACCAACAGAAAGGTTAAATGAGTTCTCGTAACAGGACACAACAGCAC
+CAACAATACATGAAAAAAAAAAAAGA
+>307ec816-d48a-46c5-93dd-4035dde1d324
+ACATCGGTACTTCCGTTCAGTTACGTATTGCTGGTGCTGTTGCGTCCTGTTACGAGAACT
+CATTTAACCTACTTGCCTGTCAGCTCCTCTTCTCATTAACAAACTGCATCTTCCCTACTG
+CTACTGATAGTTGTAGGTAATCCGTCGTTGACTGTACACAGCTTCATTAGTTTTGCAATA
+CTCCGCAAGCCGGAGGATGTTGACATTCTGGTTGGCCTGTAGTGGGGCCACGGCTATATT
+GTCTGTTGCCGCTATTTACTAACCCAAAACTACACTGCCAATAACGGCACCTATAAAAGC
+GCTTTGTCTCCCTTCCCCTCAGACGTGGACACAGACCCTTGGATCTTGGGATGGAATCGC
+CAAGAAGAATTGAACAAAGTAGTCAGTGTTCACAGTATGCCTCTAAGCTGGGGCTTTTGC
+ACACGCCTCCTTGTCCTTGGGCATATTCAGGGAGCAATTTGACTATGATTGACCCTGTCT
+GAGACAGTGTATACATTGACACCTTATCTCCTGTCACTACAATTTCCTGCAGCTACAGGC
+CTGCCAAATCCAAGGGAGCTTGTCAGACGGATACAACAATATCAGCATAATCCGAGTTAT
+CCAGCATCAAGTGCTGGGATCTGGTGAAGGTTTGGTGGAGCCCATATTGCGTCCTGGATG
+GCTGGTCGGGATCAGACCCTTCTACCAAATGTTTTCTAATTTGCTAAACAGGTGAACTAA
+CTTAAGCAGTTGAGATGGATCATTATCTGAGTGTCATGTTGGATTCAGGAAGCAGGTGAA
+CACCACAGTCTTAGGGATGCAACTTATTTTCTGAAGGATTGTATTTGGCAATGTTGTGTC
+TCTTCTCTAGCTTAGGGTAACCTCTGCAATATCAGCACCAACAGAAAGGTTAAATGAGTT
+CTCGTAACAGGACGCAACAACTCCAGCACAACTCCCCTTCAACTCCCA
+>8b9c1924-15ee-4da4-960b-c1f9de201685
+ACGGTATGCTTGCTTCGTTCAGTTACATGTTACTGAATTGCTGTTGCGTGTCCTGTTACG
+AGAACTTTCGATTGCTCCTACTTGCCTGTCGCTCTATCCTTCTCATTAACAAACTGCTGC
+ATCTTCCCTACTGCTACTGATAGTTTGTGATAATCCGTCCCATTTGACTTCATACACAAC
+TTCATTGGTTGCAACAATATATAACCGGAGGAGGATGTTCGGCAGCATTCTGGTTGGCCT
+GTATTGGGCCGCAGCTGCTGGTATCTATTATATGTTACCCAACCCAAAACTACTGTATGG
+CACCTATAAAGCGCTTTTGTCTCCTTCCTCAGACTTTTGGACACGGGCCCTTGAGATCTT
+GCCGGATGGAATCGCCAAGGAGTGGTACAAAGTAGTCAGTGTTCTGTTATGTATGCCTCT
+AATGGAGACTTTTGCACACACCTCCTTATCACTTGGGCATATTCGGGAACATTTGACTAC
+CAATTGACCCTATGCGAGACGGTGTATACGATGACTGCCTTATCTCCTGTCACTACAGGT
+TCCTGCAGCTGCAAGGAGGTACCGTCAAGGAGCTTGTGTCAGACCGGATACAGCTCCAAT
+ATCAACATAATCCGAGTTACATCAGCATCAAGAGTGCTGGGATCCTATTGGTGAAGGTTT
+GGAGCCCATATTGCGTCCTGGATGAGCTGGTCGGGACCAGACCCTTCTACCACTATTTTA
+TTTGCTAAACGGGTGAACTAACATAAGCCGGTTGAGATGGATCATTATCTGGTGTCATGT
+TGATTCCAGGAAAACAGGTGAACTGCAGTCTTAGGGATGCAACTTAGTACTGAAAGAGTT
+GTATTTGGCAATGGTGTCTCTTCTCCAGCGGAAAAGTAGAGGTAACCTCGCAACCATCCT
+TTCCAAACAGAAAGGTTAAATGAGTTCTCGTAACAGGACGCAACAGCACCAAACAGCCCA
+TGAG
+>a6f90ea9-42d4-47c2-b988-f805ca7a154b
+ACGGTAACGCTTCGTTCAGTTTACGTATTGCTGGTGCTGTTGCGTCCTGTACGAGAACTC
+AATTTAACCTACTTGCCTGTCGCTCTATCTTCTCATTAACAAACTGCATCTTCCCAACTG
+CTACTGATAGTTGTGATAATCCGTCAGTGACTTCATGCAGCTTCATTGGTTTAACCAATG
+CTCTCCCTTACAGCCTTGGAGGGATGCTGGCAGCATTCTGGTTGGCCTGTGTGGGGCCGC
+AGCTGCTGTTATCTGTGCCGCTGTTGCAACCCCAAAACTACTGCCAATAGCGGCACCTAT
+AAAGCGCTTTTGTCTCCTTCCTCAGACGTGGACACAGACCCTTGGATCTTGGATGGAATC
+GCCAAGAGGAGTGAGCAAGTGATCGGTGTTCTGTTATATGCCTCTAATGGAGACTTTTGC
+ACACCTCCTTATCCTTGGGCATATTCGGGAGCAATTTGATATGGTGACCCTGTCTGAGAC
+GAGGTGTATACATTGACTGCACTTATCTCCTGTCACCAATTCCTGCAGCTGCAAGGCCTG
+CCGTCAAAGGGGAGCTTGTCAGACGGATACAGCTCAATATCAGCATAATCGAGTTATCAG
+CATCAGAAGTGCTGGGATCCTGGTGAAGGTTTGGAGGCCCATATTGCGTCCTGGATGAGC
+TAGCGGTCGGGATCTCCAGACCCTTCTACTGATGTTTTTCTAATTTCATGGTGAACCCCT
+TTATAAGCAGTTGAGATGGATCATTATCTGGTGTCATGTTGATTCAGAGCCAGGTGGAGC
+ACAGTCTTAGGGATGCAACTTATTTTCTGAAAGGATTGTATTTGGCAATGGTGTGTCTTC
+TCAGCTTAGTGAAACACCTCGCAATATCAGCACCAACAGAAGGTTAAATAGGTTCTGTAA
+CAGGACGCAACAGCACCAGCAATACGTAGCA
+>eb35cfa9-2726-4109-a157-398a32a4d5d8
+CTGTACTTCGTTCAGTTACGTATTGCCTTTCAATTTGCTGTTTGCGTCCTGTTACGAGAA
+CTCAGCACATTTAACCTTTCTGTTGGTGCTGATGTGCAGGGTTACCTCTACTAAGCTGGA
+GAGACACACCATTGCCAAATACAATCCTTTCAGAAATAGAAGTTGCATCCCTAAGACTTG
+CGAGTTCACCTGCTTTTCCTGAATCAACACTTGAAGGCACCCAGATGAGTCATCTCAGCG
+CTGCTTATAGTTGGTTCTGTTTGCCAAATTAGAAAAACACGGGTAGAAGGGGTCTGGATC
+CCGACCGAAATCATCCAGGACAATGGAGGAAACCAAACCTTCTACCGGGAGGATCGCGCT
+TCGATGCAGTAACTCGGATTATGCTGATATTGAGCTGTATCGCGTCCCGACAGCTCCCAT
+GACGGCAGGCCTCTTGCTTCTTGAGATTGTAGTGACAGGAGATAAGGCAGTCCAATGTGT
+ACCTCGTCTCAGACGGGGTCAATCCTGGAGAATCAAATTGCTCCCGAGTATGCCAGGATA
+AGGAGGCGTGTGCAAAAGCCCCATTAGAGGCATGCTCCCAACAGAACACTGACTACTTTA
+TACACTCCTCTTGGCGATTCCATCCTGAAGATCCAAGGGTCTGTGTCCACGTCTGGAGGG
+AACTAAAAACATAGGTGCCATAGATTATTGGCAGTGTAGCGCTCAGGGTTGCAGCTGCGC
+TTGGCACAGATAACAGCTGCGGCTAATACAGGCCAACCAGAATGCTGCCAGCATCCTCCG
+GCTTAAGGGAGAGCATTGCTGCAACCAATGAGAGCTGTGCATGTGGGGAAGTCACCGACG
+GATTATGCAACTATCGAGGTAGCGGTTGGGAAGATGCAGCAATTTGTTAATGAAGATAGA
+GCGACAGGCAAAGTAGGTTGTTAAATGGAGTTCTCGTAACGCAGGACACCAACAGCACCA
+GCAATACGGCA
+>9ac4d524-83af-4bac-a4c7-76be1b9cb92c
+ACGGTACTTCGTTCAGTTACATTATTGCTGGTGCTGGTAGACCCTGTTACGAGAACTCAT
+TTAATACTGCCTGTCGCTCTATCTTCTCATTAACAAATTGCGTCTTCCTACTACTACTGA
+TGGTTGTGATGGCTCCGTCGGTGACTTCATTACACAGCTTCGTGGTTGCAACAATGCTCT
+CTAACAAACCAGATGTTGGCATTCTGGTTGGCCACATATTGGGGCCGCAGCTGCTTTCTG
+TTATCTCTGTACCCTTGCTATTCCCATTTACCCAAGAGCTACCAATAACGGCACCTGCTC
+AAACGCTTTTATTCCTCCAGACGTGGACACAAGACCCTTGGATCTTGCGGATGGAGTCAT
+AGAAAGTGAGCAAGTGGTCAGTGTTCTGCCATGCCTCTAATGGAGACTTTTGCACACCTC
+ACCCATCCTTGGGCATATTCGGGGCAATTTGACTATGATTGACCCTTCTGAGACGAGGTG
+GCATAGCCATTGACTGCCTTATCTCTATCATAATTCACCCAGCTACGGAGGCCTGCGATC
+GAGAGCTGTCAGGCTGGATACAGCTCAATATCAATCCCGAGTTATCAGCATCAAGTGCCT
+GGATCTGGTAGAGGTTGGAGCCCATATTGGGCATCCTGAGTGAGCTGGTCGGGATCCAGG
+CCCTTCCCTGCTGTTTTTCTAATTTGCTAAACAATTGTGAACTAACTATAAGCAGTTGAG
+ATGGATCATTATCTGGTGTCCTATTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGG
+ATGCAACTTATTTTCGAGTTGTATTTGGCAATAGGTGTCTCTTCTCTCCAGCTTGGTGAA
+GGTAACCTCGCAATATCAGCACCAACAGAAAGGTTAAATGAGTTCTGCCTCGTAACAGGA
+CTGGCACAAACAATGCAATAACTAC
+>2751bdce-4bb4-4d0a-ba04-6fcaaa1b7f93
+TTTAACATCAGTATGCTTCGTTCAGTTACGTATTGCTGGTGCTATTTGCGTCCTGTTACG
+AGAACTCATTTAACACTCTGTTGGTGCTGATGGCCCGAGGTTACCTCTACTAAGCTGGAG
+AAAAGAGACACACCATTGCCAAATACAATCACTTTCCAGAAAATAAAGTTGCATCCTAAG
+ACTGCAGTTCACCTGCTTTCCTGAATCAACATGACACCAGATAATGATCCATCTCAACTG
+CCCATAGTTGGATTCTTGTTTAGCAAATTAGAAAAACACGGGTAGAAGGGTCTGGATCCC
+GACCAGCTCATCAGACGCAATATGGGCTCCAAACCTTCTACCAGGATCCCAGCACTTCTG
+ATGCTGATAACTCTCCCGGATTATGCTGATGATGAGCTTTGTATCCGTCCTGACAAGCTC
+CCTTGACGGCGAGCCTCTTGCAGCTGGGAATTGTAGTGACGGGGAGATAAGGCAGTCAAT
+GTATACACCTCGCCTCAGACAGGGTCAATCTTAGTCAAATTGCTCCCAGGCCATGCCCAA
+GGATAGGAGCGTGTGCAAAGCCCCCATTAGAGGCATATAACAGAACACTGACTACTTTGC
+TCACTCCTCTTGGCGATTCATCCACCAAGATCAGGGTCTATGTCCACGTCTGGAGGGGAA
+CCAAAAAGCGCTTTATAGGTGCCGTTATTGGCAGTGTAGCTCTTGGGGTTGCAACAACGC
+ACAAATAACAGCAACTGCGGCCCTAATACAGGCCAACCAGAATACTTAACATCCTCGGCT
+TAAGGAGAGCATTGCTGCAACCAATGAAGCTGTGCATGAAGTCACCGACAGTTATCACAA
+CGCTATCAGTAGCAGTAGGGAAGATGCAGCAATTTGTTAATGAGAAGATAGAGCGACAGT
+AGAGTAGGTTAAATGAGTTCTCGTAACAGGACATAACAACTTTTTCAACAATAAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/variants.ref.fa	Fri Dec 01 22:13:14 2017 -0500
@@ -0,0 +1,15 @@
+>cluster_0
+TCATTAACAAATGCTGCATCTTCCCTACTGCTACTGATAGTTGTGATAATCCGTCGGTGA
+CTTCATGCACAGCTTCATTGGTTGCAACAATGCTCTCCTTAAGCCGGAGGATGTTGGCAG
+CATTCTGGTTGGCCTGTATTGGGGCCGCAGCTGCTGTTATCTGTGCCGCTGTTGCAACCC
+CAAAGCTACACTGCCAATAACGGCACCTATAAAGCGCTTTTGTCTCCTTCCTCAGACGTG
+GACACAGACCCTTGGATCTTGCGGATGGAATCGCCAAGAGGAGTGANCAAAGTAGTCAGT
+GTTCTGTTATATGCCTCTAATGGNGGCTTTTGCACACGCCTCCTTATCCTTGGGCATATT
+CGGGAGCAATTTGACTATGATTGACCCTGTCTGAGACGAGGTGTATACATTGACTGCCTT
+ATCTCCTGTCACTACAATTCCTGCAGCTGCANGAGGCCTGCCGTCAAGGGAGCTTGTCAG
+ACGGATACAGCTCAATATCAGCATAATCCGAGTTATCAGCATCNAAGTGCTGGGATCCTG
+GTGAAGGTTTGGAGCCCATATTGCGTCCTGGATGAGCTGGTCGGGATCCAGACCCTTCTA
+CCGATGTTTTTCTAATTTGCTAAACAGGTGAACNAACTATAAGCAGTTGAGATGGATCAT
+TATCTGGTGTCATGTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGGATGCAACTTA
+TTTTCTGAAAGGATTGTATTTGGCAATGGTGTGTCTCTTCTCCAGCTTAGTAGAGGTAAC
+CTC