Mercurial > repos > rnateam > targetfinder
changeset 0:773fdd1a02ea draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
| author | rnateam |
|---|---|
| date | Wed, 21 Dec 2016 17:31:28 -0500 |
| parents | |
| children | c9d56748fbde |
| files | TargetFinder.xml test-data/Antirrhinum_majus.mRNA.EST.fasta test-data/ath_miRNAs_predicted_targets.txt test-data/ath_miRNAs_test.fa |
| diffstat | 4 files changed, 110 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TargetFinder.xml Wed Dec 21 17:31:28 2016 -0500 @@ -0,0 +1,73 @@ +<tool id="targetfinder" name="Plant small RNA target prediction tool" version="1.7.0"> + <requirements> + <requirement type="package" version="1.7">targetfinder</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + targetfinder_threads.pl + -f $f + -d $d + -c $c + -t "\${GALAXY_SLOTS:-12}" + $r + -o $output1 + ]]></command> + <inputs> + <param label="Input small RNA sequences file" help="(-f) FASTA-format" name="f" type="data" format="fasta" /> + <param label="Target sequence database file" help="(-d) FASTA-format" name="d" type="data" format="fasta" /> + <param label="Prediction score cutoff value" help="(-c) DEFAULT = 4" name="c" type="float" value="4.0" /> + <param label="Search reverse strand for targets?" help="(-r) Use this option if the database is genomic DNA." name="r" type="boolean" falsevalue="" truevalue="-r" checked="false" /> + </inputs> + <outputs> + <data name="output1" format="data"/> + </outputs> + <tests> + <test> + <param name="f" value="ath_miRNAs_test.fa"/> + <param name="d" value="Antirrhinum_majus.mRNA.EST.fasta"/> + <param name="r" value=""/> + <param name="c" value="4.0"/> + <param name="t" value="1"/> + <output name="output1" file="ath_miRNAs_predicted_targets.txt" compare="contains"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +TargetFinder will computationally predict small RNA binding sites on target transcripts from a sequence database. + +This is done by aligning the input small RNA sequence against all transcripts, +followed by site scoring using a position-weighted scoring matrix. + +**Input** + +-f Input small RNA sequences file (FASTA-format). + +-d Target sequence database file (FASTA-format) + +**Output** + +Each predicted target site is printed out separately. +The output consists of two parts. + +The first is a description line and the second is a base-pairing diagram of the target and small RNA (query) sequence. + +The description line contains the query name, the description line from the target sequence database, and the target prediction score. + +The base-pairing diagram has the target site sequence on top in 5'-3' orientation and the query sequence on the bottom in 3'-5' orientation. + +Between the target site sequece and the query sequence are base pair symbols. + +A ":" (colon) symbol represents an ordinary Watson-Crick base pair, a "." (period) represents a G:U base pair, and a " " (space) represents a mismatch. + +If a small RNA is predicted to target a sequence more than once, each target site will be output as separate output. +]]></help> + <citations> + <citation type="doi">10.1016/j.cell.2005.04.004</citation> + <citation type="doi">10.1371/journal.pone.0000219</citation> + <citation type="doi">10.1007/978-1-60327-005-2_4</citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Antirrhinum_majus.mRNA.EST.fasta Wed Dec 21 17:31:28 2016 -0500 @@ -0,0 +1,23 @@ +>gi|51053470|gb|AJ787245.1|AJ787245 EST AJ787245 Antirrhinum majus whole plant Antirrhinum majus cDNA clone 018_1_01_o13, mRNA sequence. +CTCATACACCATGCTTTAAGCTTCATTGTACGGTCATCTTTCTCTTTTACCCTTGTTCTT +CCTTTTCTCTCCAAAAAGAAAAAAATGGATCCCAACATGCAAAACATGATGTCCTCTTAC +TTAAAAATCAAGAAACTTGTGGGAGATGAAGGGAGTGATTTTGAGGAGGAAGAAGAAGGT +GAAGACGAAGAAGAAGAAGAACAAGAAAGGGTTGTTAAAGTGAACTTTGCAGAGTCACAA +TTGAAGAAGAAAAAATTGAATCTTGGTGAAGGGTCTGGTGGAAAAAGTGGTGAGAAACAT +ACTGCTAGTGGTGGTGGAGTTGTGGCTCAGCCTTGTTGTTTGGTTGAGAATTGTGGTGCT +GATCTGAGGAATTGCAAGAAGTATTACCAAAGGCACAGGGTTTGTGAGGTTCATGCTAAG +GCTCCTGTGGTTTCTGTTGAGGGGTTGATGCAAAGGTTCTGTCAGCAATGTAGCAGGTTC +CATGATCTCTCGGAATTCGATCAGACAAAGAGGAGTTGTCGCCGACGTCTCGCTGGCCAC +AATGAACGGCGCCGTAAGAGTTCGCTCGAGTCTCACAAGGAGGGCAGAAGCCCAAGATAA +GGACAGCCTGATGAAACAAGTTTCCGTGTTATTGGAAAGTGTCTAGAATGCTTACTCTCT +TCTGTCACCTCGTGCC +>gi|51107699|gb|AJ792371.1|AJ792371 EST AJ792371 Antirrhinum majus whole plant Antirrhinum majus cDNA clone 018_2_11_f24, mRNA sequence. +TCTCTAATTCAGCACTGCTCTCTCTCTTCTGTCAAATAGTCCTGGGGCTCTAGAAACTCG +AACAATTTTCTTGGTACTAATGGAAACGGGCCAACCATAGTTCAGCCGTCTATTAACCCT +GGTGCTACAATTGGACAGTTTACCTGTCCCTCTTGGGGTTTTGGAGGCAACCCAGCTGAT +AACACCTCCCATGATATGCCTCCCAATCTGAATTTAGGACAATTTTCTCACTCCAGTAAC +AGTCACTATACTGGAGAGCCTGGGGTAGTCCAACTGAGCCACGGACAATTCCAGGACCTC +GATCACTCAAGAGGCTATGATTCTTCCGTTCAGGACATGCATTGGTCACTTTGAAGTATT +CCGATTCTGGACTCCCTCAATCTAGTGTTTTCAGTAACTTAAGTAAATTCCAGTGAATTA +TCAAACACCAGGGCTTTTGTGGTGTTGCCATGTGTTCTCTTAGGAATCTGAAACTTGTAT +GTGTGGGGTTATTTATGCTATTGCTTGTGGGCCTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ath_miRNAs_predicted_targets.txt Wed Dec 21 17:31:28 2016 -0500 @@ -0,0 +1,12 @@ +query=ath-miR156g, target=gb|AJ787245.1|AJ787245 EST AJ787245 Antirrhinum majus whole plant Antirrhinum maju, score=2.5, range=0-0, strand=1 + +target 5' AUGCUUACUCUCUUCUGUCA 3' + ::::.::::::::::::: +query 3' CACGAGUGAGAGAAGACAGC 5' + +query=ath-miR156g, target=gb|AJ792371.1|AJ792371 EST AJ792371 Antirrhinum majus whole plant Antirrhinum maju, score=3, range=0-0, strand=1 + +target 5' CUGCUCUCUCUCUUCUGUCA 3' + ::::: :::::::::::: +query 3' CACGAGUGAGAGAAGACAGC 5' +