Repository 'snpeff_from_gff_vcf'
hg clone https://toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf

Changeset 1:633d264f8888 (2018-04-16)
Previous changeset 0:abde5b0387c8 (2015-03-23)
Commit message:
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
modified:
SnpEff.pl
snpEff.xml
added:
test-data/snpeff_in.fasta
test-data/snpeff_in.gff3
test-data/snpeff_input.vcf
test-data/snpeff_output.vcf
removed:
tool-data/tool_dependencies.xml
b
diff -r abde5b0387c8 -r 633d264f8888 SnpEff.pl
--- a/SnpEff.pl Mon Mar 23 05:17:19 2015 -0400
+++ b/SnpEff.pl Mon Apr 16 08:56:29 2018 -0400
b
@@ -72,10 +72,12 @@
 close($C2);
 
 
-my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies";
+my $build_cmd = "snpEff build -c $session/snpEff.config -gff3 myspecies";
+#my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies";
 system($build_cmd);
 
-my $eff_cmd = "java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
+my $eff_cmd = "snpEff eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
+#my $eff_cmd = "java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
 system($eff_cmd);
 
 
b
diff -r abde5b0387c8 -r 633d264f8888 snpEff.xml
--- a/snpEff.xml Mon Mar 23 05:17:19 2015 -0400
+++ b/snpEff.xml Mon Apr 16 08:56:29 2018 -0400
[
@@ -1,9 +1,15 @@
-<tool id="snpEff" name="SnpEff" version="4.0">
- <description>predicts SNP effect from a genomic VCF file</description>
+<tool id="snpEff" name="SnpEff" version="2.0.0">
+ <description>Predicts SNP effect from a genomic VCF file</description>
  <requirements>
- <requirement type="package" version="4.0">snpEff</requirement>
+ <requirement type="package" version="4.3.1">snpEff</requirement>
  </requirements> 
 
+        <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+        <stdio>
+            <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+            <exit_code range="1:" level="fatal" />
+        </stdio>
+
  <!-- 
      You will need to change the path to wherever your installation is.
  You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
@@ -21,43 +27,56 @@
  <data format="txt" name="log" label="Log file"/>
  </outputs>
 
- <help>
-
+    <tests>
+        <test>
+            <param name="vcf" value="snpeff_input.vcf"/>
+            <param name="genome" value="snpeff_in.fasta"/>
+            <param name="gff" value="snpeff_in.gff3"/>
+            <output name="output" file="snpeff_output.vcf" compare="diff" lines_diff="4"/>
+        </test>
+    </tests>
 
-
-
+    <help><![CDATA[
 
 .. class:: infomark
 
-**Program encapsulated in Galaxy by Southgreen**
+**SnpEff** version 4.0
+  | **Please cite** "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", **Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.**, Fly (Austin). 2012 Apr-Jun;6(2):80-92.
+
+.. class:: infomark
+
+**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
 
 .. class:: infomark
 
-**SnpEff version 4.0**
+**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
 
------
+---------------------------------------------------
 
-==============
- Please cite:
-==============
+======
+SnpEff
+======
 
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", **Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.**, Fly (Austin). 2012 Apr-Jun;6(2):80-92.
+-----------
+Description
+-----------
 
------
+  | Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
+  | For further informations, please visit the SnpEff website_.
 
-===========
- Overview:
-===========
-
-Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
+.. _website: http://snpeff.sourceforge.net/
 
------
-
-For further informations, please visite the SnpEff_ website.
+------------
+Dependencies
+------------
+SnpEff
+        SnpEff_ 4.3.1, Conda version
 
+.. _snpeff: https://anaconda.org/bioconda/snpeff
 
-.. _SnpEff: http://snpeff.sourceforge.net/
-        </help>
-
+    ]]></help>
+    <citations>
+       <citation type="doi">10.4161/fly.19695</citation>
+    </citations>
 </tool>
 
b
diff -r abde5b0387c8 -r 633d264f8888 test-data/snpeff_in.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snpeff_in.fasta Mon Apr 16 08:56:29 2018 -0400
b
b'@@ -0,0 +1,606898 @@\n+>Chr3\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTAAACCCTAAACCCTAAA\n+CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT\n+AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTCAATCCTAACC\n+CCTCAATCCTAAGCCGTCTGCAGTGGCCATCGCAGGGTGAGGTGGGTGGAGGGTGAGTGA\n+GGACTAAGTCATCCCTTCGCCGCCTACCCGAGGACCACGATGCCGCCTCCACCCAAGGAC\n+CGTGTTGTGCCATCGTCTGCTCCCCTACTCCGTCCAAATCTAGGAGGGAGAGGAGGGGAG\n+TGCCGCCTCCACTGTCGTCTGCGATGGCCACCGCTGACGGCTCCCCTCCTCTATTCAGAT\n+CTAGGAAGTATGGAGAGAGGGACGGAGGGGAGTAGTGTGGTTAGGCAGTGAAGGGTGAGG\n+TGAAGGGAAGGAGAGGTGGGTGGAGGGTGAGTGAGGACTTACTGCAGTGCGGAAGGTTGC\n+GGATGTTTAGGGTTAGGGTTTTAGGGTTTAGGGTTTAGTTAGTTTTGTACCACAAATCAA\n+TAGAGAAACTAAGAAAATGACAATAAAACTAGAGCAAATCATTTTAATCCCAGCAAGCAA\n+ATAGATGCACGGTTACATCATATAGAAGCATAAATTTATCTACCAAAAATATATGGAGAA\n+TTGGTAACCGTGCAAAATTGACTATGAGTTCTAAAACAATTACGAATCAGTCCCTAATCT\n+CAAAGTAACCTTCAATTTTAAAGACCCTAAGGGACTCAAGTGCAAAAGTACCTAATTGTA\n+TCAGAATTTATCTAACTAGAAAAATTTAGTGAAATCCCACATTAGTCCACCGATCAAGCA\n+CTCCTTAGGTGTCAGTCAGTGAAACATCCATCAAAACTAAAGCAGGTGAGTCATACCGAG\n+AACGATCTAGTGAGTACGACAAGTCACTAATGAGAGAAGTCGCAAACGACACTGCCAGAG\n+TTACAGGTAAGGCATACCTCTTATCTTACGACTTATGGAACATACCGATAAGGTATACCT\n+TCACGTATACGGATTGTCCCTGTAAATGTCGCATGGAAACCACTTCAAATTATGGAAAAT\n+ATCTCTACGAGTCAAGTGATTTCCAAAGTCCTACTCAGAAGGGATAGATTTTCTATTATA\n+CAGTACCAGGTCCGATATCCCCAAACCTTTCTTGGGGATCAAGATGATCCACGATATAAA\n+AGGGACCCCTGGGAGGAGTTCAAGGCATCTAATTCAATCGCCAACACACCCACCAAAGTT\n+TACGAAGCCAAAGTATACGGAATCAACTCGCCAGGAGATCTCGTCGAATCCCTTGATTAC\n+GATCTCATCAGTACCATCTGTTTCGACTACTCTCTTTGTAATCTGTTCTCATCATCATCA\n+ATCTCATATAAACTAGATTAGGGCTGTCGGTGACATGGGACCGGGAGTATCATGACTAGA\n+GGCTTGGGCAGCCGCGATCACCCACGTGGCCTGACCCCCTCGGGGGGGTCGGGCCCGAGG\n+GTGATGTGGCTGCCCCTCCCTTTGTCTCCCCCAGGGGTCGGATCGCTCCCGTTTCAGCCC\n+CGAGGGCCGGGGCGCCCCGACCCCCTGTGGGTTTGGCGCCACGTATATGGGTTAGGTGAG\n+GACAGCGGGGCTCACCTAACCGCATTTATTGCGGGGTTAACGAGCGCGTCACGCCGCATG\n+TAATGCAGCGCAGCGCGCTCGCTTATCCGGTCCGTGACCGGGCGCAGCGTGTGACCGGTC\n+ACAGACCGGTCAGATCGCGGGTTAGGTGGTGGCAGGTGGCCTGTTACACGCCTCGCCCCG\n+TCCCGTCGGATTGATGAGAGCCTCCAGGCACTTGTCCCTAGCCGGAGACGGCGTGCCAGC\n+TCCTGAAGATGGCACGTCGGTCCCGGTCAGATATATGCCAGGCTTCATCCCAACCATTGC\n+AAGGAAGTCATTGTATGAAGAAGGGCAGACATGCAGCTTGCTAAACTGACGCGTGGTGGA\n+CGAGAGTGACCGGTCTGTGACTGGTCTGACGCCTGTCATGTCATAGGCAGACAACCGCGC\n+TCCCGTTTTGCACCTCCTTCCAGCGGAGTGGAGGTAGGTATGACCCATCCCATCGGAGGG\n+TCATTCGGACAGCAGCCATTGCAAATCTCCGCCCATTTAATGAGGGAGGACAGGGTTATC\n+CCAATGTCAGACGAAGGTACAAGCCAAGTTTTGGTCAAAGTAGGATGGATCCCCACCCAA\n+AAGAATGGTAGGTAGAAATAGTGTATGTGGTATCCCCTTGAGATATAAAAGGAGGACCAT\n+ACCTACCAAGAGAAGAAGGAGAAAAGGAGACGAAAAAAGAGAGAGAAAAAAAAAGGAGGA\n+GGACAACTGAGAGAACACCTAGACTCTCTAGCTCTTCTGCTCTCTGTAATTCCTTCACAC\n+TCAGATCCACCAGAACACAGGAGTAGGGTATTACGCTTCTCAGCGGCCCGAACCTGTCTA\n+CATCGCCCGTGTCTTGCGCGTTTGCTCTCTCGTGTACATTCCACAGATCGAGGGCTTAGA\n+ACCTCACTTAGCGCCCCCGGCCGAACCGGCAAAGGGGGGCCCGCGCGGTCTCCCGGTGAG\n+GAGCCCCACGCTCCGTCAAGGGCTATTACCTGATAAGGGACCTGAACCAGTATAATCCTT\n+GTTTTTTGTCTGCTTGATGTCGTACTACGTAGACCCTCGTTCCAACGTACCCCAATACTC\n+TACTTATTCGGTCCGCGAGTATCACTCGTCGACAAATATGGCCATTTTTATTCTTCTTTA\n+TTTTTTCTTCCCATATTTTCTACTTGTCTTTTGATTTCTCATTGGTATAGGAAGACTTTT\n+GA'..b'TCCCTTGCCATAATGAGGAGAGGGAGAGTGA\n+GGAGGAGGAGGAGAGGGAGAGCAGCTGCTTCTCCTACTCTTGGACGGGTGCGGCGTGGAG\n+TGGCGGGGGCCATGGATGACGTCGACGATGACGGCGGCGGTCGGTTTGGCATGGAGCGGG\n+GGCAAGGCGGCAGCGCGTGGCATCGGCGGTGCAAGGGCTGATGGCGGCGGCGACCGAGCG\n+GCGAGCGCGCGCGCGGGAAGGGCGACCGGCGAATTCAAACGGCGGCGGCGGGAATCAGCG\n+CCGAGGAGAGGAGTTCGACGAGAGAGAGAGAGAGAGAGAAAGAAGACGAGAGAGCGAGCG\n+CACGCGAGGGAGGAAGGAGCGGCTGAGGGAGAGAGATGGGCCGAGGGAAAAAAAACGGCC\n+CACAACAACCGAGGGAGGTAAACTAGACTTTTTCCGAGGAAATCGATTCGGAGGGATACG\n+AGATTTGGAAATTGAATTTTGGATTTCGAACTTGAGGCTTGGTCTGACAAAGCAGGGAGG\n+AGTCAAGGGGAAGCACCCAAGCGAGAATTCGGTATTTCTTTGGAGCAGAGTTATACTCGG\n+CGGTCCGAGGGATTAGATGAGAGGGATTCAAGTGAGACCTATCTTTGGAGTTGGGACAAC\n+GGTATGGGATAGGTTCCAAGGGTAGATAGGTAGAGGGACGGATAGATTGATAGATAGATA\n+GACAGCTGGTTAGATAGATAGATAGATAGATAGGTAGATCGATACATAGACAGATAGATC\n+GGCTGATGGGTAGATAAACGAATAGGAAGATCGATAGACAGATCGATGGATAGATAGTAG\n+GTAGGCAGATTGATTAGAGAGAGGGAGAGAGAGATAGGGACGAAAGAATCGACGATTGAT\n+TTCAGGATGTTGATTTCAGAGACTTGAATCGGAATTGGAATTTGAGGTGAAGGATTTTGA\n+TTTCGATGAGAGGGATCAACGGGATTTGAAATGAGATCCTTGGCACAACTTAGACTCGCA\n+CACAAAGAACGAAAATTTTCGCAATTAGGATTTTGCCGAATTAGTTTTTAACGACTCACG\n+AAAAGCGGAGCGTTACACCGGTGCAGGGGTCCCACATGTCGGCAGAGGTTGAGTGGTGGT\n+GGAGCATCGGTGCGTCAGCCGTGGATTCATAGGTGGTGAGCGGCGGGTGAAAACCCAGCC\n+CAGCCTTGGTCGGACCGACAACAATGGTATTCCCCCTCCTGAGGGCGTTGTCATGCTGTC\n+TCACCCCTCAAGGGTGGTTGTCGGGCGAAAGCCCAGTCTTGGCTCCTTTGAGCCTTGACG\n+GACGGTGGTGGCGGTTTTTCGTCGCTTCTCTTCTTGAAGACGTTGTTTTGGCACCCCCTT\n+GCTGTGGGCGATCTCGTCTGTGTTCCTTTGTTGGTCTAGCGGTGGTCGGTCACGCTTAGC\n+AGCGGCCGGTCTGATGCTTGCCTTCTCCCGGACTTGTGTATTGGCGCTGTCGGTGTGTGG\n+GTGGTGGTATGTTTTTTACTTTTTCCTGGTTACGACCCTTCAGGGTTGTAATCTTGTAAT\n+TTTTTTTCTGCTCTATCAATAGAACTTCGCACCGTCTCGTGCGAGTTGTTCAAAAAAAAA\n+CACTAGTGACGGAGCGTGGGGCTCCTCACCGGGAGACCGCGCAGGCCCCCCTTTGCCGGT\n+TCGGCCGGGGACTCAGGGAGAGATTCTAAGCTCTCTGTATGTGGAAGGCTCGCGAGACAG\n+GAAACACACAAGACACGGGCGATGTATACAGGTTCGGGCCGCTGAGAAGCGTAATACCCT\n+ACTCCTGTGTTTTGGGAGATCTGTGTATGAAGGAGCTACAAAGTATCAGCCAGGCTCTCC\n+CTTGTTCTGGGTTTCTCATCTGGAAAAGTCCAGTCCCCCCTCTCAGTGGGCAAGGTCCTC\n+CTTTTATATATTAAGGGGATACCACATGCACCATTTCTCTCTTTTTTTGTAGGGACTTAC\n+CCCCCCTTTTCATAAATGAACGGAGATTTGTATAGTTGCCGTCCGAGTCACCTTCTGATG\n+AGACGGCCCACAACTACCTCCACTTTCGCCGGGAGCAGGTGCGACGTGGAATCGTGGCTG\n+TCTGCTGACGACATGACCGGTATCAGACCAGTCACGTCGGTCATTCTTGTCCACCACGTG\n+TCAGCTTAGCAATCTACATGCTCGCCCTTCTTCACACAACATCTTGCCTGTAATGGTTAG\n+GATGAAGCCTGGCATATATCTGACCAGGACTAACGTGCCATCTCTGGGAGGTAACACGCT\n+AGCTCCAGCTGGGGACGAGCGCCTAGAAGCCCTCGTCCTGACGGGATGGGGCGAGGCGTG\n+CGTCAGATCGCCTGTCGCCACCTAACCCGCGATCTGACCGGTCTGTGACTGGTCACAGAC\n+CGGATAAACGAGTGCACTGCACTGCGTTACATGCGGCGTGACACGCTCAGCCAAACCGCA\n+ATAAATGTGGTTAGGTGAGCCCCACTGTGCTCACCTAACCCATACACGCGGAGCAAAAAC\n+CCACGAGGGGTCGGGGCGCCTCGGCCCTCGGGGCCGAGGGGGGTACGGCCCGACCCCCTC\n+GGGGGGACTAAGAGGAGGGCGAACGCATCACCCTCGGGCCCGACGTCCCTCGGGGGTACC\n+AGGCCACGTGTGCGATTGTGTCTGCCTCAAACCTCTAGTCATGATACTCCTGATCCCATG\n+TCACCGACAACTAGAAACACAAAAGACCAAGAAAAATTTAAGAGACATTACGAGTATTGT\n+ATTATGGAGTTTTTTCCGCAAATTTCTCTATGTCCAAAATTTGTTGCTCAGCTTCTTCGA\n+GTCGTAATTGCAGATCCTTCAACATTCTTTTTTCTTCTCGTACTCAGTCATCGTCTCCAT\n+AGTAGTCAAATCAGATCTCTACATAATTAAAGAAAATAGCAAGTCCTTAAGCGCTTGTGG\n+ATATAATATATTGAAACAAAGTGTACATGCTTTCAGTATGCACTTTTTAACTTTTCGTTA\n+GCTGATGCAAGCTGCAGCTCCAATGTTTTAATTCTCTCTGTTTGGGACGAACATGTTTCC\n+TGTATTGAAAATACATTAGTTGCACCGATTGTAGTAATTAGACATTGAATCAATTAGAGC\n+ATAATTTAAGATGAACAGATGTTTGTAATGAAAGGTCGGGACTAAGATCATACCTTTTCC\n+AAATCTAGCTGCATCTTTACAGAGTTAGCATGGTGTTTCAAACCATTCATTGTTTCTACC\n+ATAGTGTTCTTCTCTTTCTGCAGCATTGCTATTATTTCACCATTCTTCGTTGCATTTGTA\n+GATTGCTGTTATACTGTTGCAAACTAGTGTTGTATTCTTGAAGCCTCTTATTTGTGTCCT\n+GAAGCATCTTGAGATTTAAAAGGTTTAGGGTTTAGGGTTTAGGATTTAGGGCTTAGGGCT\n+TAGGGCTTAGGGTTCAGGGTTCAGGGTTCAGGGTTCAGGGTTCAGTGTTCAGGGTTTTGG\n+GTTCGGGGTTTAGGGTTGAGGGTTGAGGGTTTAGGGTTGAGGGTTTAGGGTTGAGGGTTT\n+AGGGTTGAGGGTTTAGGGTTGAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG\n+TTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTA\n+GGGTTTAGGGTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTATAGGGTT\n+TAGGGTATAGGGTTAGGGTATAGGGTTTAGGGTTTAGGGTATAGGGTTTAGGGTTTAGGG\n+TTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTA\n+GGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG\n'
b
diff -r abde5b0387c8 -r 633d264f8888 test-data/snpeff_in.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snpeff_in.gff3 Mon Apr 16 08:56:29 2018 -0400
b
b'@@ -0,0 +1,93257 @@\n+##gff-version 3\n+Chr3\tMSU_osa1r7\tgene\t4465\t6944\t.\t+\t.\tID=LOC_Os03g01008;Name=LOC_Os03g01008;Note=expressed%20protein\n+Chr3\tMSU_osa1r7\tmRNA\t4465\t6944\t.\t+\t.\tID=LOC_Os03g01008.1;Name=LOC_Os03g01008.1;Parent=LOC_Os03g01008\n+Chr3\tMSU_osa1r7\texon\t4465\t5039\t.\t+\t.\tID=LOC_Os03g01008.1:exon_1;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\texon\t5174\t5422\t.\t+\t.\tID=LOC_Os03g01008.1:exon_2;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\texon\t5530\t6136\t.\t+\t.\tID=LOC_Os03g01008.1:exon_3;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\texon\t6235\t6302\t.\t+\t.\tID=LOC_Os03g01008.1:exon_4;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\texon\t6398\t6460\t.\t+\t.\tID=LOC_Os03g01008.1:exon_5;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\texon\t6545\t6944\t.\t+\t.\tID=LOC_Os03g01008.1:exon_6;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tfive_prime_UTR\t4465\t4636\t.\t+\t.\tID=LOC_Os03g01008.1:utr_1;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tCDS\t4637\t5039\t.\t+\t.\tID=LOC_Os03g01008.1:cds_1;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tCDS\t5174\t5422\t.\t+\t.\tID=LOC_Os03g01008.1:cds_2;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tCDS\t5530\t6136\t.\t+\t.\tID=LOC_Os03g01008.1:cds_3;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tCDS\t6235\t6302\t.\t+\t.\tID=LOC_Os03g01008.1:cds_4;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tCDS\t6398\t6460\t.\t+\t.\tID=LOC_Os03g01008.1:cds_5;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tCDS\t6545\t6573\t.\t+\t.\tID=LOC_Os03g01008.1:cds_6;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tthree_prime_UTR\t6574\t6944\t.\t+\t.\tID=LOC_Os03g01008.1:utr_2;Parent=LOC_Os03g01008.1\n+Chr3\tMSU_osa1r7\tgene\t8502\t9736\t.\t-\t.\tID=LOC_Os03g01012;Name=LOC_Os03g01012;Note=tetraspanin%20family%20protein%2C%20putative%2C%20expressed\n+Chr3\tMSU_osa1r7\tmRNA\t8502\t9736\t.\t-\t.\tID=LOC_Os03g01012.1;Name=LOC_Os03g01012.1;Parent=LOC_Os03g01012\n+Chr3\tMSU_osa1r7\texon\t8502\t9736\t.\t-\t.\tID=LOC_Os03g01012.1:exon_1;Parent=LOC_Os03g01012.1\n+Chr3\tMSU_osa1r7\tfive_prime_UTR\t9496\t9736\t.\t-\t.\tID=LOC_Os03g01012.1:utr_2;Parent=LOC_Os03g01012.1\n+Chr3\tMSU_osa1r7\tCDS\t8671\t9495\t.\t-\t.\tID=LOC_Os03g01012.1:cds_1;Parent=LOC_Os03g01012.1\n+Chr3\tMSU_osa1r7\tthree_prime_UTR\t8502\t8670\t.\t-\t.\tID=LOC_Os03g01012.1:utr_1;Parent=LOC_Os03g01012.1\n+Chr3\tMSU_osa1r7\tgene\t13193\t16729\t.\t+\t.\tID=LOC_Os03g01014;Name=LOC_Os03g01014;Note=expressed%20protein\n+Chr3\tMSU_osa1r7\tmRNA\t13193\t16729\t.\t+\t.\tID=LOC_Os03g01014.1;Name=LOC_Os03g01014.1;Parent=LOC_Os03g01014\n+Chr3\tMSU_osa1r7\texon\t13193\t13961\t.\t+\t.\tID=LOC_Os03g01014.1:exon_1;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t14082\t14233\t.\t+\t.\tID=LOC_Os03g01014.1:exon_2;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t14307\t14402\t.\t+\t.\tID=LOC_Os03g01014.1:exon_3;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t15125\t15187\t.\t+\t.\tID=LOC_Os03g01014.1:exon_4;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t15378\t15446\t.\t+\t.\tID=LOC_Os03g01014.1:exon_5;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t15539\t15641\t.\t+\t.\tID=LOC_Os03g01014.1:exon_6;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t15749\t15820\t.\t+\t.\tID=LOC_Os03g01014.1:exon_7;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t15940\t16028\t.\t+\t.\tID=LOC_Os03g01014.1:exon_8;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\texon\t16133\t16729\t.\t+\t.\tID=LOC_Os03g01014.1:exon_9;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tfive_prime_UTR\t13193\t13618\t.\t+\t.\tID=LOC_Os03g01014.1:utr_1;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t13619\t13961\t.\t+\t.\tID=LOC_Os03g01014.1:cds_1;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t14082\t14233\t.\t+\t.\tID=LOC_Os03g01014.1:cds_2;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t14307\t14402\t.\t+\t.\tID=LOC_Os03g01014.1:cds_3;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t15125\t15187\t.\t+\t.\tID=LOC_Os03g01014.1:cds_4;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t15378\t15446\t.\t+\t.\tID=LOC_Os03g01014.1:cds_5;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t15539\t15641\t.\t+\t.\tID=LOC_Os03g01014.1:cds_6;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t15749\t15820\t.\t+\t.\tID=LOC_Os03g01014.1:cds_7;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t15940\t16028\t.\t+\t.\tID=LOC_Os03g01014.1:cds_8;Parent=LOC_Os03g01014.1\n+Chr3\tMSU_osa1r7\tCDS\t16133\t16288\t.\t+\t.\tID=LOC_Os03g0'..b'Os03g64400.4:exon_8;Parent=LOC_Os03g64400.4\n+Chr3\tMSU_osa1r7\texon\t36399569\t36400100\t.\t+\t.\tID=LOC_Os03g64400.4:exon_9;Parent=LOC_Os03g64400.4\n+Chr3\tMSU_osa1r7\texon\t36400846\t36401705\t.\t+\t.\tID=LOC_Os03g64400.4:exon_10;Parent=LOC_Os03g64400.4\n+Chr3\tMSU_osa1r7\tfive_prime_UTR\t36394773\t36395125\t.\t+\t.\tID=LOC_Os03g64400.4:utr_1;Parent=LOC_Os03g64400.4\n+Chr3\tMSU_osa1r7\tfive_prime_UTR\t36395244\t36395344\t.\t+\t.\tID=LOC_Os03g64400.4:utr_2;Parent=LOC_Os03g64400.4\n+Chr3\tMSU_osa1r7\tfive_prime_UTR\t36395599\t36396095\t.\t+\t.\tID=LOC_Os03g64400.4:utr_3;Parent=LOC_Os03g64400.4\n+Ch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b
diff -r abde5b0387c8 -r 633d264f8888 test-data/snpeff_input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snpeff_input.vcf Mon Apr 16 08:56:29 2018 -0400
b
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b
diff -r abde5b0387c8 -r 633d264f8888 test-data/snpeff_output.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snpeff_output.vcf Mon Apr 16 08:56:29 2018 -0400
b
b'@@ -0,0 +1,3106 @@\n+##fileformat=VCFv4.2\n+##fileDate=...\n+##source=PLINKv1.90\n+##contig=<ID=3,length=19999036>\n+##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"\n+##SnpEffCmd="SnpEff  -o vcf -no-downstream -no-upstream myspecies -s ... ... "\n+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: \'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO\' ">\n+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: \'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected\'">\n+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: \'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected\'">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tc88dcbba.0\t0b7d031b.0\t16ef3c90.0\t26863647.0\t7f32098d.0\t608b0d34.0\t46aa9c6a.0\td00c1e13.0\t8366125c.0\ta358fb3f.0\t2a5ee06d.0\tdf3c89f8.0\t78f9e9fe.0\t04aca4b5.0\t04704bb4.0\t5cf82125.0\t559cd294.0\t98ca16ae.0\t1865f890.0\t66391666.0\t824bd841.0\t971d8d35.0\t1580b445.0\t3476f3f1.0\t6fe1d5f1.0\t727d7321.0\t8a1459b3.0\t1a210383.0\t2aa697f5.0\ta7596568.0\t41872470.0\td9a92db4.0\t66b6164a.0\t5a43ae22.0\t6ac8c69b.0\t3afe78bc.0\tbf19b73d.0\td7e9eece.0\t82e8b7f7.0\t60121701.0\t6cf8dce4.0\t3051c486.0\t59afa5e3.0\t68b91064.0\tae03e236.0\tddaead61.0\taa6cd0c1.0\te1d9a122.0\tfb625f89.0\tcb0723a4.0\t98042619.0\taca14ce9.0\tbada3969.0\t5efeb5b6.0\tfe614ecb.0\tbea7cbcf.0\t1abb6b2c.0\t4506b36e.0\taddc58a4.0\tf5f3d6ea.0\te1838272.0\td2dd5d08.0\t4874cc49.0\ta6e508e5.0\t61544ce0.0\t429e439a.0\t522427a2.0\tb41ea6b3.0\t773db8bf.0\tce7eb496.0\t2eafa96f.0\t533385bb.0\t1f8b989f.0\t44fe4cf1.0\t07990ed9.0\tf40ea464.0\tc7913661.0\tc54cc672.0\t66c5c186.0\tc111198a.0\t5b45a727.0\tde954805.0\t2552833e.0\tc840a160.0\t529e807c.0\t1fb8be6d.0\ta85f295d.0\tcb0c4d54.0\tc3b20632.0\t3f0e6324.0\t178d96de.0\t225b17eb.0\t99d33763.0\td10e2929.0\t8f99b9e2.0\tf6801eb5.0\te2606999.0\tb308ee1b.0\ta7e6bc0f.0\t84e1a141.0\tbcea78dd.0\te1d1c3b0.0\t01a58510.0\t9c00ac3a.0\t71ad2583.0\tea2ae002.0\tbc730b70.0\t9c62b49e.0\t5da42fd9.0\t3b7bddf8.0\t45388f1b.0\tcd33864f.0\t28dd8a58.0\t1de0e087.0\t07fd6392.0\tf8c60a5c.0\t25cdd8ae.0\t23b0b44c.0\t484b2a0f.0\t82e17a03.0\tbe2b0b83.0\t260c1d61.0\te30161a0.0\t115e701d.0\t4c13a3a3.0\t08beaab3.0\t68f6c96b.0\t2d661c20.0\tfb2aa5d5.0\t2ece01ea.0\te048f5ff.0\tee58d650.0\t5872a595.0\t5975119a.0\te3fc5497.0\ta51b2a39.0\td66638c8.0\ta5ef5ab7.0\t7d71b69f.0\tb4b4df33.0\t14d89242.0\t9bdaf6eb.0\tc949dc7c.0\td4dd88ed.0\t8fa373e8.0\teaa3a28a.0\t8609fb0e.0\ta6d8f1fd.0\tbe814f56.0\tabc6960f.0\t832b2be7.0\t5776533f.0\t3d3f5b4e.0\tbc700e39.0\t946e0202.0\t47c2ea40.0\tc86d6702.0\tb95ce243.0\t2e05f839.0\t79ec00de.0\tf292fe0a.0\ta65ecc2d.0\t2b962329.0\t718e09f3.0\t0a5fbba4.0\t89d2c5a0.0\t61d7b167.0\t2bfcbe44.0\t90bc17da.0\t65329b91.0\te069425a.0\t5325e87e.0\t7578b606.0\t6fb127b9.0\t3b8476cc.0\tc8fc9010.0\tfd96414a.0\t7f0e7041.0\ta0c41ad0.0\t1e5e8456.0\tab4a346a.0\t77bec15a.0\t2bca2f34.0\t9651d67d.0\t9a5569b2.0\tb961cc90.0\te42dd51d.0\t911f856a.0\t53e1db9a.0\te5b216b3.0\t18484bd4.0\t64f24c90.0\t9cbb223a.0\tf7e1ce6e.0\t9e44e293.0\teac19fb8.0\t76f56677.0\t87621330.0\tdc2cf39b.0\t17627a92.0\t7126c359.0\tc20dfc59.0\tcbd6b346.0\tf30e146b.0\t1510e4aa.0\tcf44b628.0\tbd7aaa87.0\te8f708a5.0\t2b4e06fe.0\t3eb8fab5.0\taeed4684.0\t328163e1.0\tc7aeb39f.0\t3e58f34c.0\tcc0ef8cf.0\t30646147.0\t192e24ab.0\t5ef1be74.0\t71d5fcf4.0\t714ac141.0\t0f6a67da.0\ta796716d.0\ta8319fc6.0\t93387d96.0\t5384be83.0\t8fafd383.0\tcff871e8.0\t2a7724c1.0\t773e969e.0\t743f41c1.0\t1a946dc6.0\t9ac72c9e.0\t5505a767.0\t8cd35626.0\tfdd98970.0\t86556239.0\t44aeff79.0\tc7d2513e.0\t2a9d8d47.0\t39dd7feb.0\tc0936cf1.0\t5aa7968d.0\t73c4fdfb.0\t5ae0bd70.0\t122a975b.0\t2b81cf74.0\t9b2223bb.0\tbf18cbae.0\t16463092.0\t7a723d9e.0\tc8a73fe7.0\t5b144b9c.0\t3aa518'..b'0/0\t0/0\t0/0\t0/0\t./.\t0/0\t1/1\t./.\t1/1\t./.\t0/0\t0/0\t./.\t1/1\t1/1\t1/1\t1/1\t1/1\t./.\t1/1\t0/0\t./.\t0/0\t./.\t0/0\t./.\t./.\t0/0\t./.\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t./.\t0/0\t0/0\t./.\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t1/1\t./.\t0/0\t./.\t0/0\t./.\t./.\t0/0\t0/0\t1/1\t0/0\n+3\t19991345\tSNP-3.19989855.\tA\tG\t.\t.\tPR;ANN=G|intergenic_region|MODIFIER|LOC_Os03g36030-LOC_Os03g36050|LOC_Os03g36030-LOC_Os03g36050|intergenic_region|LOC_Os03g36030-LOC_Os03g36050|||n.19991345A>G||||||\tGT\t0/0\t0/0\t1/1\t0/0\t1/1\t1/1\t1/1\t0/0\t0/0\t0/0\t1/1\t1/1\t0/0\t1/1\t1/1\t0/0\t1/1\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t0/0\t1/1\t1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b
diff -r abde5b0387c8 -r 633d264f8888 tool-data/tool_dependencies.xml
--- a/tool-data/tool_dependencies.xml Mon Mar 23 05:17:19 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="snpEff" version="4.0">
-        <repository name="package_snpeff_4_0" owner="iuc" changeset_revision="6bc55957927b" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>