| Next changeset 1:5a4b00c84f50 (2017-11-11) |
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Commit message:
Imported from capsule None |
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added:
rnabob.xml test-data/F22B7.fa test-data/r17.bob test-data/r17.des test-data/trna.bob test-data/trna.des tool_dependencies.xml |
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| diff -r 000000000000 -r cd00b4fe6552 rnabob.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnabob.xml Mon Dec 22 09:08:31 2014 -0500 |
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| b'@@ -0,0 +1,218 @@\n+<tool id="rbc_rnabob" name="RNABOB" version="2.2.1.0">\n+ <description>Fast Pattern searching for RNA secondary structures</description>\n+ <requirements>\n+ <requirement type="package" version="2.2.1">rnabob</requirement>\n+ </requirements>\n+ <version_command>echo "2.2.1"</version_command>\n+ <command>\n+<![CDATA[\n+ rnabob \n+ \t-q\n+ \t$fancy\n+ \t$compStrands\n+ \t$skipOverlapping\n+ \t$descriptorFile\n+ \t$sequenceFile > $stdout\n+]]>\n+ </command>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />\n+ <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />\n+ </stdio>\n+ <inputs>\n+ <param name="descriptorFile" type="data" format="txt" multiple="false" label="Motif Descriptor File" help="This file contains the description of the motif for which to search"/>\n+\t <param name="sequenceFile" type="data" format="fasta" multiple="false" label="Sequence File" help="This file specifies the sequence in which the motif will be searched"/>\n+\t <param name="compStrands" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Also search on complementary strands" help="-c : Search both strands of the supplied sequence"/>\n+\t <param name="skipOverlapping" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Skip overlapping matches" help="-s : This is a workaround to avoid a problem in the DNABANK, overlapping matches will be ignored"/>\n+\t <param name="fancy" type="boolean" checked="false" truevalue="-F" falsevalue="" label="Show Alignments" help="Display full alignments to pattern"/>\n+ </inputs>\n+ <outputs>\n+ <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="descriptorFile" value="r17.des" />\n+ <param name="sequenceFile" value="F22B7.fa" />\n+ <param name="compStrands" value="True" />\n+ <param name="skipOverlapping" value="False" />\n+ <param name="fancy" value="False" />\n+ <output name="stdout" file="r17.bob" />\n+ </test>\n+ <test>\n+ <param name="descriptorFile" value="trna.des" />\n+ <param name="sequenceFile" value="F22B7.fa" />\n+ <param name="compStrands" value="True" />\n+ <param name="skipOverlapping" value="False" />\n+ <param name="fancy" value="False" />\n+ <output name="stdout" file="trna.bob" />\n+ </test>\n+ </tests>\n+ <help>\n+**What RNABOB does**\n+\n+RNABOB allows searching a sequence database for RNA structural motifs.\n+The probe motif is specified in a *descriptor* file,\n+which describes its primary sequence, secondary structure, and tertiary constraints.\n+The source in its original packaging can be found at http://selab.janelia.org/software/#rnabob.\n+\n+-----\n+\n+**Sequence database format**\n+\n+RNABOB is currently restricted to reading sequence files in FASTA format. \n+The command line version of RNABOB can also read sequence files in GCG, EMBL, GenBank and other formats.\n+\n+-----\n+\n+**Descriptor file syntax**\n+\n+The descriptor file syntax is fairly powerful, and allows a great deal of freedom for specifying \n+RNA motifs. The syntax is therefore a bit complicated.\n+\n+The descriptor file has two parts: a **topology** description and an **explicit** description.\n+\n+The first non-blank, non-comment line of the file is the topology description. It defines the \n+order of occurrence of a series of single-stranded, double-stranded and related elements. Each \n+element must be given a unique name (a number, typically) and must be prefixed with \'**s**\', \n+\'**h**\', or \'**r**\', indicating single-strand, helical, or a relational element. Helical and \n+relational elements are paired to other elements, which are suffixed by a prime, **\\\'**.\n+\n+For example::\n+\n+\t\\\n+\t\t\th1 s1 h1\'\n+\n+desc'..b'of position do not match on left and right sides, the program will refuse to accept \n+the descriptor.\n+\n+Relational elements have an additional field which specifies a "transformation matrix" of four \n+nucleotides, specifying the rule for making the ``r\'`` pattern from the ``r`` sequence in order \n+``A-C-G-T``. For example, the transformation matrix for a simple helix is ``TGCA``; if you allow \n+``G-U`` pairs, it is ``TGYR``. RNABOB allows ``G-U`` pairing by default and uses the ``TGYR`` \n+matrix for helical elements.\n+\n+For example, the explicit description of our hairpin might be:\n+\n+::\n+\n+\t\\\n+\t \t\th1 0:0 NNN:NNN\n+\t \t\tr1 0:0 R:N GNAN\n+\t \t\th2 0:0 **NC:GN**\n+\t\t \ts1 0 UUCG\n+\n+This describes a stem of 6 to 8 base pairs, in which the 4th pair from the bottom of the stem must \n+be a non-canonical GA pair. Note that, in general, the left side of the primary constraint for \n+helices and relational elements is redundant, and should be given as all N. In some cases it is \n+convenient to constrain the right side to require a particular base pair (GU, for instance) at one \n+position.\n+\n+A note on mismatches: The split format for helices and relational elements works like this. The \n+number on the left constrains the primary sequence match of the left side of the primary \n+constraint. The number on the right constrains the match of the right side of the primary \n+constraint, *after* that side has been constructed according to the sequence on the left. In other \n+words, the number on the left constrains the mismatches in primary sequence only, while the number \n+on the right will constrain the number of mispaired positions in the helix.\n+\n+Finally: any line that begins with a pound sign \'#\' is a comment line, and will not be interpreted \n+by the pattern compiler.\n+\n+**Options**\n+\n+The behavior of RNABOB can be modified by use of the following options:\n+\n+*Complement*: Selecting this option will cause RNABOB to search for the pattern also on the \n+complementary strands.\n+\n+*Skip*: This is a workaround to avoid a problem in the DNABANK. There are some sequences in the \n+database which have long stretches of ambiguous sequence (N\'s). Descriptors with no primary \n+sequence constraints will match these garbage sequences at many, many positions, and generate huge \n+outputs. This option toggles a search strategy that skips forward a pattern-length rather than a \n+single base when a match is found, thus printing out only a single match when overlapping matches \n+are found. \n+\n+**Examples**\n+\n+The following example descriptors included in the source distribution \n+(http://selab.janelia.org/software/rnabob/rnabob.tar.gz):\n+\n+\t- trna.des - a general descriptor of a tRNA structure\n+\t- r17.des - descriptor of the consensus binding site for the r17 phage coat protein\n+\t- pseudoknot.des - description of a simple pseudoknotted structure\n+\n+An example cosmid ``F22B7.fa`` from the *C. elegans* genome sequencing project is also provided \n+for running these descriptors against.\n+\n+::\n+\n+\t\\\n+\t\t# trna.des\n+\t\t#\n+\t\t# Generalized descriptor of a tRNA cloverleaf. Doesn\'t\n+\t\t# find them all though. \n+\t\t#\n+\n+\t\th1 s1 h2 s2 h2\' s3 h3 s4 h3\' s5 h4 s6 h4\' h1\' s8\n+\n+\t\th1 0:2 NNNNNNN:NNNNNNN\n+\t\th2 0:1 *NNN:NNN*\n+\t\th3 0:1 NNNNN:NNNNN\n+\t\th4 0:1 NNNNN:NNNNN\n+\t\ts1 0 TN\n+\t\ts2 0 NNNN**********\n+\t\ts3 0 N\n+\t\ts4 0 NNNNNN*\n+\t\ts5 0 NN********************\n+\t\ts6 0 TTC****\n+\t\ts8 0 NCCA\n+\n+Running RNABOB with ``trna.des`` against ``F22B7.fa`` searches the top strand of the cosmid for \n+the above motif. ``trna.des`` hits twice, once on each strand. (F22B7 has several other tRNA genes \n+in it which the pattern fails to detect - this is *not* a pattern to use for tRNA genefinding!).\n+ </help> \n+ <citations>\n+\t<citation type="doi">10.1093/bioinformatics/6.4.325</citation>\n+\t<citation type="bibtex">@UNPUBLISHED{rnabob,\n+author = {Eddy S.R},\n+title = {RNABOB: a program to search for RNA secondary structure motifs in sequence databases},\n+note = {}}</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r cd00b4fe6552 test-data/F22B7.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/F22B7.fa Mon Dec 22 09:08:31 2014 -0500 |
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| b'@@ -0,0 +1,806 @@\n+>F22B7 921215/f22b7.seq\n+GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT\n+GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT\n+TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT\n+TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC\n+GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA\n+ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG\n+AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA\n+CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA\n+TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC\n+AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA\n+GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC\n+AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC\n+CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA\n+AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC\n+GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT\n+AACACATATTGACCATTTGGTTTGTTCAAATCAGAACAAATCTTAGCGAG\n+CATAAAGTTAGATGCGATTCCAGCAGAACATGTTAATCCCGTGAGTTGTT\n+CAACTCGAAATCGAATTTCTCGAACAGCCTCCTCTCGTCCAGTTCCGAAC\n+TCCACATGGTCGTAGTAGATTTTCCGCGATTTTTCGCATTTTGGACAGAT\n+CGATTCTTCGATTTTCAAGTCTTCCAAAGTATTTTCATTCTCGTCGAAAC\n+GGGGTAACCAACATGGACAATCTCCGCCGAATCTGTGACGCTTGAAGGTT\n+TCTAGTAAGCAAATAGTTTTTTGTTAATAATCAAATCTAAATCACTAACT\n+TTTTTCTGTATTACTTGCCACATAGTCTGTCAAATCTATAAATGCCTCAT\n+CCAATGACATCATTCCAACATCCGAATCGTATTCCATGAAAATTTGTGAA\n+AATTGGCGACTGACTTTAGTGTATTTAGGGTAATTTCCTGGAACAATCGT\n+TAGACTCGGACAAAGTTTATTTGAGATGAAGCCAGGCATTCCAGCACGGA\n+CTCCAAAACGGCGAGCCAAGTAGTTGGATGTGCTCTGAAAGAATAGATTT\n+AAAGCTTTTCCGAAATCGAAAATTTACTTTTCAAATTGAGTTAGGTGCTT\n+ACCAGCATTGCCGATGAGCCTACGGCCATAGGAACTGTTCTCAGTGCAGG\n+ATTATCTCTCATTTCAACTGCGGCAAAATAAGCATCCATATCTATACAAA\n+CACAGTCTCTTGATAAATCTCTAGATGATTCCAGTTTCATCTCAAGATTC\n+TCCATCTGAAAATTGGAAATTTGCTCTAAGTAAATTTATTAGCTTTTAAA\n+ATACATACCAGTATCTCAGATTTTTGTCTTTCTTCTCTGGTTGCTGTTTG\n+CAAACGATTTTTGATTTCTAAAACTTTCTCTTCAATTCTTGATTGTTGTT\n+TTTTGGAAAACGACGAGTAGGACGCTGATGTGTTTTCTTCGATGACTTTC\n+GTGATTTTCTCCTTATCCAGTCCATTCATTCCAGCTTTATTATCGTTGAA\n+AGTCAGCATTTTTCACGAAAAAGAGCCGGATTTTGAAATTCGCGGAGAAA\n+CTCCACTGATTGTGAGTGTGCAAATGCGCGTAATGGTGTACTTACGTACA\n+TCGGCAACACATTTGACGACATATCAGAAAGCGGCGCCAAATTAGAAGTT\n+GAGTGCGCGAGAAAAAACTACGCGTTAACCGCCAATTTTCACTTCCCCAC\n+AGATCTGTCTCGAGATTCTCGAGTCATTTTTCAAGTTTATTTGTTTGTCA\n+GCGGTTGTTTTATTGAAGATTTGTAAAATTTATAACAAAATGTGCAATAG\n+TCTATTAAACCTCGTGAGATATTTGAAGAAACTTTCCCCGTTTTAAATAT\n+TTCGTGTATTCGTGGAGATCGCGGGAATGTTTTGCCTGTTTCCGTAAAAT\n+TCCTCTATTTCTTTTATTTTTGCTTGCAATTTTCGATTCATTTCAGAAGT\n+TTCCACATTCGCAAAACGAATGGACGTCTCTTATTACGATGGTCCCAAGG\n+ATGAAGTCGCCGAAGCAATGCTGAAAAGCGCGGTGACGGCCATGAGATTG\n+GGACAATACGAGGATGGAAAAGGACGCTTAGAGGAGATAATGGAGTTCGG\n+AACCTCAAATTTTCAACTACTTGGTACAATCTACATGTATTACGGAAGAG\n+TGTGCAGGCATTTGAACCATGATGCCAAGGCCTTGGAGTTTTTCGAACAT\n+GAGTTGAACATGTTCAAGTAAGTGAATCACAAAAATGAGCTGGACATTCT\n+ATAACCTTAATTTTTCAGATTGATCTTCAACTACCCAGAAGCATGTGATT\n+CCACACGTCGCATCGTCGAGCAGGCACTCAAAATGGGAAAGTTCCCCAAG\n+GCTCGACGGTTTGCTGAGGATCTCATTGATTACACCAGCAATAAGAAGAA\n+CGGAGAGAAGTATATCGGTCAAGCTCGAATTTTGTTCGCTTCCGTGTGCC\n+TCGAAGGATGTGAAAGAGACGTCGAGAGTAATCAAGATGAGAAGAAGAAG\n+CTTTTGTCAATATGTGCTGAACAGATTGCAGCCGTGAAATTGTTCAACGA\n+GAATAATACGGAAGGAGCTGTGTCTGAGACCAAAATCATGTTACTTGAGG\n+CGAAATGCTTGTCACTAGACGAAAAATACGAGGAATCGCGTCGCAAGTAT\n+CAAGAATGCATCGATTTTGCCATCAAAACAGACCAGTTTGAAGCAGTTCA\n+CATCGCCTATTACGACAAGGCTCTATATGCTGAGACAGATCTTCTTTTCT\n+TTATTATCAGAGATCTCAGGTAATTTTTAGTTTTAACGATTAATAAAAAT\n+ATCAATTCTTTATTCACAGAAGTGCTCTCTTCTACGCCACGAAATTCGGA\n+AAAGAGCGAGATGTAGTCAAATATAAGTCGAAGCTATCCGAAGAGATGCT\n+GAGAAATGGCGAATTCCACGAAGCATATCTCTACGGATTGGAAGCGCTTG\n+TATCGATTCGGAAGCTTGGATTGAACGAATACATTGGAGATGTGTTGCTT\n+ACAATCGCAAAGTGCCTCATTGCACTTGGAAAAAGACGCCAAGCTGCTTA\n+TTTTATCATCTTGGGGAGTGTTCTGACCATCAACCAAAACAGTTTCAAAC\n+TGTTCTACGAGCAGATCGACGTGGCGATGAATCAAGAGAGAAGCGAAACG\n+GCAACTGATCAAGATGTATGCCTCGCAATTGATTCGTCTCCTGATCCGAC\n+ATCCTCGAATGACATGATTAATAAGTTCGTCGTCGAACTGGAGCACGCAA\n+CAAATGTGGAAACCTGGGAAATGATTGTCAACGGAATCATTGACGACCAG\n+AAGAAACCAGTGGCGATCGAAAAGAAAGAGAACGAGGAACCCGTAGACAT\n+GATGGATCTCATTTTCAGTATGAGCTCACGTATGGATGATCAAAGAACTG\n+AACTGCCTGCTGCCAGATTCATTCCGCGTAAGAAATGTTATAAATAAGCG\n+TATAAGTATGCAAATTTATATTTTTCCAGCTCGTCCAGTGTCATCGGCAT\n+CG'..b'AGGTAGGTGTTGTAAGCAGGCA\n+GACATTTTGAACCCTACATGGACACCCCATTTCAAATAACTACTATTAAA\n+ACATAGTTTTCTTAAAAAAGTATTTAATTTGTTTCCCCACCCAATTGCTC\n+TTAATAATCCTCATTGGTTCTCCTAGTTTTACTCTTTTGTTCCCATTTCC\n+CTTTTTTTGCAATTCAAAACACATCCAGTTTTGAGAGAGAGGTCTCTCTC\n+TCTGTCCCTCTCTACCTCCCCCTCTCTCTGTAATTATCGACTTTGGGGAC\n+GAAATGTCAGTTCATTTGTGGAAATAGTTTATGAATCGGAGAGACTTTAG\n+ACACTTTGAACAAACCGTGTCGTCGTCAGTGACGAGACACAAACACAGGA\n+AGTTTCGTTGAATATGTTGATGTTTCTGTTGACGTTTCGTTCCCTAGTTT\n+TTAGAGATTGAGAGCATCTAAGGATTAAGGTTCAATGTTTCAAGATTTAA\n+AGTTTTGAAACATAAGTAACAGAGTAAATGATATGATTTAGATAATTTTC\n+TTATTTTTTAATCTGGCAAGCACGCTCAACTAACAAAACACGAATCCGAC\n+AATCAGTCAAACATCTTAAACTTTTTAAAAAATTGTTCATTCTTTATAAG\n+AGCGAATTTCAAATTTAAAAAAAACTTTAATTAAGCTTCAGGTCAAGCAA\n+TTAGGCGTTATTATTAATTCTGGCAAGTTTCCGTTTTTCAGATATAATCA\n+TTTCAATTTCGATTCTTTCTTCAAAGTGTCTGGAAAAAATGCTCTTTTTT\n+AATAATTTCGCCGAATCTAATAGTTCTAAAATTTTATGTTGAAACGATCA\n+ATTCTATAACAGTATATTCAAAAATAACCTCACTAAACTTGAATTTTTTC\n+CAAAAAAAAGCATTCAAAGTGAGCAAATAGTTTTGGTAATACAGGTGGCT\n+ACAAATTTTCTGTCAAAATGTTCAATACACAAAGTGTGAGCAAGAGCAGA\n+ACCAGTTTTCAAACATATTGCTCTCAGTTCTCACTTTCATTTTTGTTTGT\n+ATTAGAGGCTCATTGAGCAATAGCAACTTGAACTTTACTTACTGTTTGTA\n+ATAGCTTAACTGTTCACATTTTTACTAAAACTTTGCAACCTATAGGTATA\n+CCTAATAATTGGGTTTTTCAATTTTGTATGAGAAATCACATCCCGAAACT\n+GAATGGAAACTTTCTGATTAAAATGGATATCACTTCAAACATAGTGTCTT\n+TTAATATTGTCTAAGCCTGTATGACAGTGATAATTTCTAATAAAGAGGCG\n+CAGAGAAATTAGATAATGACCGATAATGATGAGATGAATGAATGTAATGA\n+TGTGGGAAAATAGATAATAGAATAAGAAGTGTGGGCATAATGATTTAGAT\n+GATAGAAGCGTTCAGTCTAGGAATCATTTCAAGTCAATATCACTAATTAT\n+CTCATTTATTTTTGTTCCTTTGATTTATTCGTTTTGGTAGGGCCGTTTCA\n+TCTTAAAGCGTATATTCAAAACAATTAAAAAATCGTTTTTGAAGTCTTCC\n+AAGTAAAAATAAATATCTGCTTTGTGCCTATATTGCGCACCTATCATTTA\n+ATTTCTTAAATGGGGCGTAGCAATTTTGGACTTCTGCTTCAATATCTTCA\n+AAATGATCCCAATAGACCGAATTTCATAATGTGACTCCTCGAAAATTTCT\n+TATGAAGATACAACATTTTAACACTGTTTTCTTTCATAGTGTCCAACGCC\n+TGCCTTTTTCCTACACTAGTTTTTTTTTCAATATCCTTGCAAGTGCACCT\n+GCAAGAAAAGTTTAACAAAAGTTCTTAAACTTAAAAAAGTAGGTGGTAGG\n+CAGGCACGTAGGTGCGCAGGTATGTAGCCAATAGATTCTCAAAATATAAT\n+TATAAAAACTCTGCATTTCTTTTTATTCATCCTAAAAGCGCATTCTACTC\n+AAAACCCAGTCACATGCTCTATTCACAAAAGTCAATTTTTTTTCATCTGC\n+TCTCCGCATAAACTCTTGCTTCCAATTTCCAGATGCATTTAATGTCACGT\n+GCGTTCACTTTTTTCCCTTCAAGCTTCCAGAACAAAAAAGTCTTGTGATG\n+TTTCGCTCAGAAATTTGTTTGAATAGATGATAATTGGATTTCGGTTGAAT\n+TATTTTTGCCATCGCATGTCCTTTCTTCAATTCTCAATTTCCAGTTTTCG\n+TGTGATTCTCCAAAAGTTTCAAACATCATCCGAATTTTCTTGTTTTTCTA\n+TTATGTCACTGATTTCCTATTTATTTTTCATATTTTTAAAGTTTTTTTTA\n+AGGGAAAATGAAAACGCCTGCAATTTTATTACTCCTATTCTTATTTATGA\n+TGAGTTTGGCACAAAGTGATGAGGAACAAAGTGGAAAGGAACCTCCCGAA\n+AAAGATGATGTTCTAGTTATTCTGGTTGGTTTTTGCCAATGTTACCATGT\n+CAGAAATGCATGCATGCCTACTTTCGGCACATCTTCGTTTTCTTTTCCCG\n+TATTCTATGTTTTAATTTTCAGGCAGAAGACAATTCGACACTATTAAACA\n+ATAACCAAACAATGTATGACCCTTCTTCCGAAGAAAAAGAAAGTGACAAA\n+CCAAAATTCAATTTATTGGAGACATATTTACCACTTTTCATATTTGTACT\n+CGATCTACCAACAGAGGATAGAGAAACTTTGAAAGCCTATGTAAAAGATA\n+AAACTTATGAAAAACTGAAATATGTAATCGATTCAAAAGTTAAAATGAAT\n+CGAAATGAGAAAAATGTCTTAGGAAGAATCAATGAATCCTTGGTACAATC\n+AATCGATAATTTGGAACATTTTGATGAGATTACTGTAGATGTGGTGAATG\n+GTTATCACGTAAGTTTGACATTTCAATGGAAAATCATCTCTCTTTAATCT\n+TTAAAATGTTTTATTTTCAAAAAAAACCTTAATATGACAATACCAAATTT\n+TCCTTCTATAACTAAATTTCTAGAATGCCTCCGTATACAACGCAATCCGT\n+TCAGTTTGGTTGAAACAATTACGTCCATTTCTGCCGCTAATTGATCAAAT\n+GGCCATTCAGCAGTATTTTGCACAAAGGTTTCAAACATCAAGCGTCTATC\n+AAAAACTATGTTTATTTTCCAGAAAATCTTCTGAAACTGAGAAAATGTCA\n+ATTTGGGCAAGATTATGGGAAAATCTGAGTGTTTGGATGTATGGAAAGAA\n+AAAATTAAACGAATGTTATGCAATGGAGCCAAAATGTGTTCGACACGCAT\n+TGGAATTGCTTAATTTTGAACAAAGGATTGATTTGGATTTAGCTGCTTAT\n+GAGAACAAGTTTGACAGTGTTGATGGAATTATTAGGGAAAGAGTGAGTCA\n+ATTTAGATATTTAAAAAATGTCAAAAGCCCCAAAACGAATTAATTTTCAG\n+CTTGGCGAAAATCGGAAAAGCAGTGAACTCGACGAATGGTTGCACAGAAA\n+TCGCCCACCAAAAGCGCTACAAGCTATTTTAGATGAGCGAAGTGACATTG\n+AGGAGGAGTAAGATATTTATATTGAATAGATAAACGTTAGATTTTTAGAG\n+CTCTTCAACGCCTTCGAGATAACGGAGTTCTGAGCTCACTCAAACATTAT\n+TACAAAGCAGTTATAGAGTCAAGAAGTCATGAAGAGCAAGAGGTAACCAA\n+TGTTTTAGATAGTTCTTGTCAATTTTCTTACGCATTTTTCGATATTCTGC\n+TAATGGGTGCAAAGTTCTAAATTGTTTTTAATTGTAGCTTTCTATATTAA\n+ACTTTCAGGACATTCGTCATTTCTTCGACATAATGAATGACACATTTGCT\n+CGTTGCTTTGACCCACTACGAGGCCAGTATCATGATTTCTAGAAAAACCC\n+TCTTTTTGACTTCTTCCTCCAT\n' |
| b |
| diff -r 000000000000 -r cd00b4fe6552 test-data/r17.bob --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/r17.bob Mon Dec 22 09:08:31 2014 -0500 |
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| @@ -0,0 +1,1 @@ + 22801 22817 F22B7 921215/f22b7.seq |
| b |
| diff -r 000000000000 -r cd00b4fe6552 test-data/r17.des --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/r17.des Mon Dec 22 09:08:31 2014 -0500 |
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| @@ -0,0 +1,13 @@ +# r17.des +# +# descriptor of the consensus binding site for the phage R17 coat +# protein: a stem with a single-base A bulge and a 4-base loop +# + + +h1 s1 h2 s2 h2' h1' + +h1 0:0 NNNN:NNNN +h2 0:0 NN:NN +s1 0 A +s2 0 AUYA |
| b |
| diff -r 000000000000 -r cd00b4fe6552 test-data/trna.bob --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trna.bob Mon Dec 22 09:08:31 2014 -0500 |
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| @@ -0,0 +1,5 @@ + 11092 11167 F22B7 921215/f22b7.seq + 28644 28556 F22B7 921215/f22b7.seq + 28643 28556 F22B7 921215/f22b7.seq + 28635 28556 F22B7 921215/f22b7.seq + 28630 28556 F22B7 921215/f22b7.seq |
| b |
| diff -r 000000000000 -r cd00b4fe6552 test-data/trna.des --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trna.des Mon Dec 22 09:08:31 2014 -0500 |
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| @@ -0,0 +1,19 @@ +# trna.des +# +# Generalized descriptor of a tRNA cloverleaf. Doesn't +# find them all though. +# + +h1 s1 h2 s2 h2' s3 h3 s4 h3' s5 h4 s6 h4' h1' s8 + +h1 0:2 NNNNNNN:NNNNNNN +h2 0:1 *NNN:NNN* +h3 0:1 NNNNN:NNNNN +h4 0:1 NNNNN:NNNNN +s1 0 TN +s2 0 NNNN********** +s3 0 N +s4 0 NNNNNN* +s5 0 NN******************** +s6 0 TTC**** +s8 0 NCCA |
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| diff -r 000000000000 -r cd00b4fe6552 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 22 09:08:31 2014 -0500 |
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| @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="rnabob" version="2.2.1"> + <install version="1.0"> + <actions> + <action type="download_by_url" target_filename="rnabob-2.2.1.tar.gz">http://selab.janelia.org/software/rnabob/rnabob.tar.gz</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>rnabob</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +Compiling rnabob requires a C compiler (typically gcc) + </readme> + </package> +</tool_dependency> |