# HG changeset patch
# User earlhaminst
# Date 1478865805 18000
# Node ID 05bc31ccc3235c494f395d0fb749bedaf8a2cdea
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
diff -r 000000000000 -r 05bc31ccc323 miranda.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/miranda.xml Fri Nov 11 07:03:25 2016 -0500
@@ -0,0 +1,56 @@
+
+ finds potential target sites for miRNAs in genomic sequences
+
+ miranda
+
+ miranda --version|grep 'miranda v'
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+ 10.1186/gb-2003-5-1-r1
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diff -r 000000000000 -r 05bc31ccc323 miranda_parser.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/miranda_parser.py Fri Nov 11 07:03:25 2016 -0500
@@ -0,0 +1,8 @@
+import sys
+
+# get hits from miranda scans
+with open(sys.argv[1]) as infile1:
+ with open(sys.argv[2], "w") as outfile:
+ for line1 in infile1:
+ if "%" in line1 and "Forward:" not in line1:
+ outfile.write(line1)
diff -r 000000000000 -r 05bc31ccc323 test-data/microrna.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/microrna.fasta Fri Nov 11 07:03:25 2016 -0500
@@ -0,0 +1,2 @@
+>gi|29565487|emb|AJ550546.1| Drosophila melanogaster microRNA miR-bantam
+GTGAGATCATTTTGAAAGCTG
diff -r 000000000000 -r 05bc31ccc323 test-data/query.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/query.fasta Fri Nov 11 07:03:25 2016 -0500
@@ -0,0 +1,57 @@
+>gi|945100|gb|U31226.1|DMU31226 Drosophila melanogaster head involution defective protein (hid) mRNA, complete cds (3'UTR only)
+TGACAAAAAATAAAAAACGAAATCCATCGTGAACAGTTTTGTGTTTTTAAATCAGTTCTAAACACGAAAA
+GGGTTGATGAAAAACGCAGAAGAATCCGAAAAACTAACTAACCGAGCAAAAACTTGACTTGAGTGTTGTT
+TGACAAATCAGGAAAGATAAAAAACAAATCATAAGAAAAAACTGCACGAAAAATGAAAAAGTTTCTAATA
+TTCAAAATCTTGCACAAGAAATACAAAATCAATTAAAGTGAACTCTAACCAAAAGTTGTACACAAAATAA
+AAAGCAAAACAAAGCAGCGAAGAACAATCACAAGAAGAGCAAAGTGCCAACAAAGTGCAGGAAGGAAGGA
+AGCGGATAAGGACAAAAAGGAAGCCAGCACACACACACACACCCACACAATGGCCGTGCCCTTTTATTTG
+CCCGAGGGCGGCGCCGATGACGTAGCGTCGAGTTCATCGGGAGCCTCGGGCAACTCCTCCCCCCACAACC
+ACCCACTTCCCTCGAGCGCATCCTCGTCCGTCTCCTCCTCGGGCGTGTCCTCGGCCTCCGCCTCCTCGGC
+CTCATCTTCGTCATCCGCATCGTCGGACGGCGCCAGCAGCGCCGCCTCGCAATCGCCGAACACCACCACC
+TCGTCGGCCACGCAGACGCCGATGCAGTCTCCACTGCCCACCGACCAAGTGCTATACGCCCTCTACGAGT
+GGGTCAGGATGTACCAGAGCCAGCAGAGTGCCCCGCAAATCTTCCAGTATCCGCCGCCAAGCCCCTCTTG
+CAATTTCACTGGCGGCGATGTGTTCTTTCCGCACGGCCATCCGAATCCGAACTCGAATCCCCATCCGCGC
+ACCCCCCGAACCAGCGTGAGCTTCTCCTCCGGCGAGGAGTACAACTTCTTCCGGCAGCAGCAGCCGCAAC
+CACATCCGTCATATCCGGCGCCATCAACACCGCAGCCAATGCCACCGCAGTCAGCGCCGCCGATGCACTG
+CAGCCACAGCTACCCGCAGCAGTCGGCGCACATGATGCCACACCATTCCGCTCCCTTCGGAATGGGCGGT
+ACCTACTACGCCGGCTACACGCCACCACCCACTCCGAACACGGCCAGTGCGGGCACCTCCAGCTCATCGG
+CGGCCTTCGGCTGGCACGGCCACCCCCACAGCCCCTTCACGTCGACCTCCACGCCGTTATCGGCGCCAGT
+GGCGCCCAAGATGCGCCTGCAGCGCAGCCAGTCGGATGCGGCCAGACGCAAGCGATTGACCTCGACGGGC
+GAGGATGAGCGCGAGTACCAGAGCGATCATGAGGCCACTTGGGACGAGTTTGGCGATCGCTACGACAACT
+TTACGGCCGGCCGGGAGCGTCTGCAGGAGTTCAATGGACGCATCCCGCCCCGGAAGAAGAAGAGCTCCAA
+TAGCCACTCGAGCAGCAGCAATAATCCAGTCTGCCATACCGACAGCCAGTCCGGTGGTACATCCCAAGCG
+GAGAGCGGTGCCATCCATGGCCACATCAGTCAGCAGCGACAGGTGGAGCGAGAACGACAAAAGGCGAAGG
+CCGAGAAGAAGAAACCACAGAGCTTCACTTGGCCAACTGTTGTGACCGTTTTCGTTTTGGCCATGGGCTG
+TGGCTTCTTTGCGGCGCGATGAAAGCGCAGGAGACGTGTAATCGAATGATCTATAGTGAAATCAGCTAGC
+CCTTAAGATATATGCCGATCTAAACATAGTTGTAGTTAAACCGTACATAAGTGCAACGAATTTATTGAAC
+TGCAGGAGCGAAAGCAGAAAGTCATTAATTCGTAAACGGATTGTTAGATACACAAACAGCCAACATACAC
+GAAGAGTGTGCCTAAGATTAAGAAGGTTGACGGGACACAAGAACAATATATTCTATCTGTCTATGGTAAC
+TGCATTTGTATTTCTAAAACGAAACGAAAGATAACAATCTTAACTGCTCAAAGTAATGAAAACTCTTAGA
+CTGGCAAGAGACTCAAATCACACTTATTTTTTTGCTGATCCATATTTTTGTACAACCTTTTGAGCGATAT
+TTACAAATTATACTAGTACAAAAAAAAGAGAGAGAGAGATAAGCAAAAGAAAACTGCCACTTTTGAGATA
+CTTTTGATAATCTTTGATTTGCATTTAATCATTTCCACACTTGCATTTTTTATAAACAACAAACAAAATT
+ACTTCCATTGTAGAACAAAGTAAACTGCAATTTCAATGTCTTCGCATTTGTAATTCCGAATTGCAAGAAA
+AACAAAAATATTTTAAATATGTTTAACTAGTAGAATTTTTTAAACGTAAGTCCACAAAAACAAGCACATC
+TAGCTTTAATTGTTGAAACAAAAGCAGAAAAAACGCAACAAAAAAATGAATGAAAATCATTAAATTAATT
+TTGTATATAGTTTTTATGCCATTTTTGTGATGTTTTGTGTCTACGGTTTATGTCATGTTATTTTAGTTAA
+ATTTCTTATGATTTATGTTTATTTGTAATATTTTTTGTCATTGTTTGTTCATCATCATATTCAAATTGGT
+CTCACAATATAATAGTTTTAAGCTCCACGCCCGGGAGATTGATGGCAAAACGATTGAAATTTGGCCAGAA
+GAGAGATAGTTTTCCCCATTCGTACACAGTCTTTTTTGGAATGCACATTAATGATCTCTCACAATGGAAA
+TTAATGAAAATTGATCTCCGCAGCTAGCCAAAGTTAAAAAAGAAATGAAGAGGAAAACATATTCTATAGG
+CAATTTTCACTATATGCTAGAATTTCCCGGGCGTTTCAATGCTAATCGAATACAGTGACATGAAAGCAAA
+CATAGCGAAAATATTAAGAAAATCAATCAAAAAGAAAGAAAAACCAATTCCCAAAAATCGCATTGATCTC
+ATGGATTTATACAATACAATTACATCAACCGTTTTTTTACAATGAGAAATGTTATAAAAAGCAGAAAGTG
+AAACACAGAAACATAAACAAAAATTAACGAAAAGCTTAGATATAAGTTCGCCAAGCGTTTTAGTTCTATT
+TTCTAGAATGTCTAAGTCGGTTTAGTGAGTTTATTAAGCTGTCTTCGGACACAAGTTTATTTGTATATAA
+GCAATATTATTTGTGTAGCCTAAGTGACAGTCCCAATCAAATCCAATCCAATATCACCCAGTCCCGGACA
+TTTCCCAGCAAAACAATAGACTATTCTCGCGTTCACATGTATCAATCTTAATTTGAATTACCACAAAATG
+AAATGAAATACTAAAACCATACACAAATGAAAAATTATTTTTGTAAATTGTTTGCATCAAGTGAGCAAGG
+GGATTAGATTAAGGAATCATCCTTGCTTTATCCCCTGCTTATTGCTAATTAGTTTTCACAATGATCTCGG
+TAAAGTTTTGTGGCCTTGCGCCCAAAAGTCGTACAGATTTTTGGTTTGCCATAAATACTCGAACAAAAAG
+TTAATGAAAAACGAAGCAAATGGAAAAAAAATCAGAATGAAACACAAGAAATTTATATTTTTGACCCAAT
+GCTACTTAATCCGTTTTTGTAATTTAAGTATCTTTACTCGACCTTGTATATAGCGCAGTTCGAATCACAG
+AATCAAATGCCATTTTTGTATAGAATTTTATTTGGTGCCAAAACAGTGACAGATAATTAAATGTCTATGA
+ACCCGTGTATTTCGCATATTATACATTTATACATATATCGTAACTTCAATGATAAGTTTGATTCTGAAAT
+TTTGTCAACTCAATTTAAGAAACATTTCTGTTGTAGTTTAGTGATTGCTAGCAGAAAGCACTTTGTTTAA
+TTGTACATTTTATATTATGCTGTAATATTTTAATATACATAAATATCATTATTGATCTCATGAATATGTT
+CATAAGACAACAAAAATTATATATATGAATACATCTATGTGTATGTGTAAAG
diff -r 000000000000 -r 05bc31ccc323 test-data/raw_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_output.txt Fri Nov 11 07:03:25 2016 -0500
@@ -0,0 +1,92 @@
+
+
+=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+miranda v3.3a microRNA Target Scanning Algorithm
+=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+(c) 2003 Memorial Sloan-Kettering Cancer Center, New York
+
+Authors: Anton Enright, Bino John, Chris Sander and Debora Marks
+(mirnatargets (at) cbio.mskcc.org - reaches all authors)
+
+Software written by: Anton Enright
+Distributed for anyone to use under the GNU Public License (GPL),
+See the files 'COPYING' and 'LICENSE' for details
+
+If you use this software please cite:
+Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS;
+(2003) Genome Biology; 5(1):R1.
+
+ miranda comes with ABSOLUTELY NO WARRANTY;
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `miranda --license' for details.
+
+Current Settings:
+=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+Query Filename: /tmp/tmpCIUFbf/files/000/dataset_109.dat
+Reference Filename: /tmp/tmpCIUFbf/files/000/dataset_110.dat
+Gap Open Penalty: -9.000000
+Gap Extend Penalty: -4.000000
+Score Threshold: 140.000000
+Energy Threshold: 1.000000 kcal/mol
+Scaling Parameter: 4.000000
+=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+Read Sequence:gi|29565487|emb|AJ550546.1| Drosophila melanogaster microRNA miR-bantam(21 nt)
+Read Sequence:gi|945100|gb|U31226.1|DMU31226 Drosophila melanogaster head involution defective protein (hid) mRNA, complete cds (3'UTR only)(3902 nt)
+=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+Performing Scan: gi|29565487|emb|AJ550546.1| vs gi|945100|gb|U31226.1|DMU31226
+=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+
+ Forward: Score: 167.000000 Q:2 to 20 R:3340 to 3360 Align Len (18) (83.33%) (94.44%)
+
+ Query: 3' gtCGAAAGTTTTACTAGAGTg 5'
+ |:||||| |||||||||:
+ Ref: 5' taGTTTTCACAATGATCTCGg 3'
+
+ Energy: -24.540001 kCal/Mol
+
+Scores for this hit:
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 167.00 -24.54 2 20 3340 3360 18 83.33% 94.44%
+
+
+ Forward: Score: 156.000000 Q:2 to 17 R:2505 to 2525 Align Len (15) (86.67%) (93.33%)
+
+ Query: 3' gtcgaAAGTTTTACTAGAGTg 5'
+ |||||| ||:|||||
+ Ref: 5' tcataTTCAAATTGGTCTCAc 3'
+
+ Energy: -20.030001 kCal/Mol
+
+Scores for this hit:
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 156.00 -20.03 2 17 2505 2525 15 86.67% 93.33%
+
+
+ Forward: Score: 155.000000 Q:2 to 16 R:2852 to 2872 Align Len (14) (78.57%) (85.71%)
+
+ Query: 3' gtcgaaAGTTTTACTAGAGTg 5'
+ ||: | ||||||||
+ Ref: 5' caaaaaTCGCATTGATCTCAt 3'
+
+ Energy: -14.570000 kCal/Mol
+
+Scores for this hit:
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 155.00 -14.57 2 16 2852 2872 14 78.57% 85.71%
+
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+ Forward: Score: 152.000000 Q:2 to 18 R:3820 to 3841 Align Len (17) (76.47%) (76.47%)
+
+ Query: 3' gtcgAAAGT-TTTACTAGAGTg 5'
+ | ||| | ||||||||
+ Ref: 5' taaaTATCATTATTGATCTCAt 3'
+
+ Energy: -14.180000 kCal/Mol
+
+Scores for this hit:
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 152.00 -14.18 2 18 3820 3841 17 76.47% 76.47%
+
+Score for this Scan:
+Seq1,Seq2,Tot Score,Tot Energy,Max Score,Max Energy,Strand,Len1,Len2,Positions
+>>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 630.00 -73.32 167.00 -24.54 1 21 3902 3340 2505 2852 3820
+Complete
+
+Scan Complete
+
diff -r 000000000000 -r 05bc31ccc323 test-data/tabular_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_output.txt Fri Nov 11 07:03:25 2016 -0500
@@ -0,0 +1,4 @@
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 167.00 -24.54 2 20 3340 3360 18 83.33% 94.44%
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 156.00 -20.03 2 17 2505 2525 15 86.67% 93.33%
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 155.00 -14.57 2 16 2852 2872 14 78.57% 85.71%
+>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 152.00 -14.18 2 18 3820 3841 17 76.47% 76.47%
diff -r 000000000000 -r 05bc31ccc323 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Nov 11 07:03:25 2016 -0500
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+ http://cbio.mskcc.org/microrna_data/miRanda-aug2010.tar.gz
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+ $INSTALL_DIR/bin
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+miRanda finds potential target sites for miRNAs in genomic sequences.
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+