# HG changeset patch
# User jdv
# Date 1518495326 18000
# Node ID f1141f6a2d6576e103310f438a30e9c0a62fc314
# Parent  b437c0a7ca04e54d4829d50093b5e299309893c0
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0ace87b59137f1ed770db97fbb33036e16205edf

diff -r b437c0a7ca04 -r f1141f6a2d65 nanopolish_variants.pl
--- a/nanopolish_variants.pl	Mon Feb 12 03:06:42 2018 -0500
+++ b/nanopolish_variants.pl	Mon Feb 12 23:15:26 2018 -0500
@@ -118,11 +118,11 @@
 open my $out_cons, '>', $fn_consensus
     or die "Failed to open output consensus: $!";
 for (@fa_files) {
-    open my $in, '<', $_;
-    while (my $line = <$in>) {
-        print {$out_cons} $line;
+    my $parser =  BioX::Seq::Stream->new($_);
+    while (my $seq = $parser->next_seq) {
+        $seq->id =~ s/^.+\K:\d+-\d+$//; # strip coordinates from ID
+        print {$out_cons} $seq->as_fasta;
     }
-    close $in;
 }
 close $out_cons;
 
diff -r b437c0a7ca04 -r f1141f6a2d65 nanopolish_variants.xml
--- a/nanopolish_variants.xml	Mon Feb 12 03:06:42 2018 -0500
+++ b/nanopolish_variants.xml	Mon Feb 12 23:15:26 2018 -0500
@@ -104,8 +104,12 @@
             <param name="fix_homopolymers" value="True"/>
             <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
             <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
+            <assert_command>
+                <has_text text="--fix-homopolymers" />
+                <not_has_text text="--calculate-all-support" />
+            </assert_command>
         </test>
-        <!-- test pre-calculated index input -->
+        <!-- test pre-calculated index input, fix-homopolymers command -->
         <test>
             <param name="input_reads" value="called.fa" ftype="fasta" />
             <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
@@ -117,7 +121,19 @@
             <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
             <assert_command>
                 <has_text text="--index" />
-                <has_text text="--fix-homopolymers" />
+            </assert_command>
+        </test>
+        <!-- test calculate-all-support command -->
+        <test>
+            <param name="input_reads" value="called.fa" ftype="fasta" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="input_bam"   value="called.bam" ftype="bam" />
+            <param name="input_ref"   value="ref.fa" ftype="fasta" />
+            <param name="input_index" value="index.tar" ftype="tar" />
+            <param name="calculate_all_support" value="True"/>
+            <assert_command>
+                <not_has_text text="--fix-homopolymers" />
+                <has_text text="--calculate-all-support" />
             </assert_command>
         </test>
     </tests>
diff -r b437c0a7ca04 -r f1141f6a2d65 test-data/consensus.fa
--- a/test-data/consensus.fa	Mon Feb 12 03:06:42 2018 -0500
+++ b/test-data/consensus.fa	Mon Feb 12 23:15:26 2018 -0500
@@ -1,2 +1,17 @@
->ref:0-921
-ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTCATTTAACCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACCAAGCTGGAGAAGCCACACCATCCGCCAAATACAATCCTTTCGAAATGGGTTTATCGAAGACTGTGATCACCGTTTTCCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCTTTAAAATTAGAAAAACACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGGCGCAGTATGGAAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGATTGCACTTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCACACCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGGGTCCAATCATGAACCAAGTTGCTCCCGGAGCCATGCCCAAGGACCAAAGAGGGCATGTGCAAGAGCCCCATTAGAGGCATAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCCATCCCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAACATAGGTGCTGTTATCGGTAGTGTAGCTCTTGGGGTTTGCAACAGCGGCGCAGATAACAGCAGCTGCAGCCCTAATACAAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAGCATTGCTGCAACCAATGAAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCTACAGCAATTTGTTAATGAGAAGATAGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGTCGCTGTACCTTTTCAACAATACGTAACTGA
+>ref
+ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTC
+ATTTAACCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACCAAGCTGGAGAAGCCA
+CACCATCCGCCAAATACAATCCTTTCGAAATGGGTTTATCGAAGACTGTGATCACCGTTT
+TCCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCT
+TTAAAATTAGAAAAACACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGG
+CGCAGTATGGAAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGA
+TTGCACTTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCA
+CACCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGG
+GTCCAATCATGAACCAAGTTGCTCCCGGAGCCATGCCCAAGGACCAAAGAGGGCATGTGC
+AAGAGCCCCATTAGAGGCATAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCC
+ATCCCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAACATAGGTGCTGT
+TATCGGTAGTGTAGCTCTTGGGGTTTGCAACAGCGGCGCAGATAACAGCAGCTGCAGCCC
+TAATACAAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAGCATTGCTGCAA
+CCAATGAAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCT
+ACAGCAATTTGTTAATGAGAAGATAGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGT
+CGCTGTACCTTTTCAACAATACGTAACTGA
diff -r b437c0a7ca04 -r f1141f6a2d65 test-data/consensus.hp.fa
--- a/test-data/consensus.hp.fa	Mon Feb 12 03:06:42 2018 -0500
+++ b/test-data/consensus.hp.fa	Mon Feb 12 23:15:26 2018 -0500
@@ -1,2 +1,17 @@
->ref:0-921
-ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTCATTTAACCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACCAAGCTGGAGAAGCCACACCATCCGCCAAATACAATCCTTTCGAAATGGGGTTTATCGAAGACTGTGATCACCGTTTTTCCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCTTTAAAATTAGAAAAACACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGGCGCAGTATGGAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGATTGCACTTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCACACCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGGGTCCAATCATGAACCAAGTTGCTCCCGGAGCCATGCCCAAGGACCAAAGAGGGCATGTGCAAGAGCCCCATTAGAGGCATAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCCATCCCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAAACATAGGTGCTGTTATCGGTAGTGTAGCTCTTGGGGTTTGCAACAGCGGCGCAGATAACAGCAGCTGCAGCCCTAATACAAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAGCATTGCTGCAACCAATGAAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCTACAGCAATTTGTTAATGAGAAGATAGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGTCGCTGTACCTTTTCAACAATACGTAACTGA
+>ref
+ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTC
+ATTTAACCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACCAAGCTGGAGAAGCCA
+CACCATCCGCCAAATACAATCCTTTCGAAATGGGGTTTATCGAAGACTGTGATCACCGTT
+TTTCCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGT
+CTTTAAAATTAGAAAAACACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAA
+GGCGCAGTATGGAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGG
+ATTGCACTTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGC
+ACACCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAG
+GGTCCAATCATGAACCAAGTTGCTCCCGGAGCCATGCCCAAGGACCAAAGAGGGCATGTG
+CAAGAGCCCCATTAGAGGCATAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTC
+CATCCCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAAACATAGGTGCT
+GTTATCGGTAGTGTAGCTCTTGGGGTTTGCAACAGCGGCGCAGATAACAGCAGCTGCAGC
+CCTAATACAAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAGCATTGCTGC
+AACCAATGAAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGAT
+CTACAGCAATTTGTTAATGAGAAGATAGAGCGACAGGCAAGTGGGTTAAATGAATGCGTA
+GTCGCTGTACCTTTTCAACAATACGTAACTGA
diff -r b437c0a7ca04 -r f1141f6a2d65 test-data/double.bam
Binary file test-data/double.bam has changed