view TargetFinder.xml @ 0:72b8f52ad50b draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 017cc50287a0190810f507cf799e02450e5c0ed5

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−<tool id="targetfinder" name="Plant small RNA target prediction tool" version="1.7.0">
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−    <requirements>
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−        <requirement type="package" version="1.7">targetfinder</requirement>
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−    </requirements>
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−    <stdio>
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−        <exit_code range="1:" />
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−    </stdio>
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−    <command><![CDATA[
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−        targetfinder_threads.pl
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−            -f $f
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−            -d $d
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−            -c $c
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−            -t "\${GALAXY_SLOTS:-12}"
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−            $r
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−            -o $output1
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−    ]]></command>
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−    <inputs>
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−        <param label="Input small RNA sequences file" help="(-f) FASTA-format" name="f" type="data" format="fasta" />
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−        <param label="Target sequence database file" help="(-d) FASTA-format" name="d" type="data" format="fasta" />
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−        <param label="Prediction score cutoff value" help="(-c) DEFAULT = 4" name="c" type="float" value="4.0" />
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−        <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" />
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−    </inputs>
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−    <outputs>
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−        <data name="output1" format="data"/>
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−    </outputs>
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−    <tests>
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−        <test>
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−            <param name="f" value="ath_miRNAs_test.fa"/>
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−            <param name="d" value="Antirrhinum_majus.mRNA.EST.fasta"/>
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−            <param name="r" value=""/>
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−            <param name="c" value="4.0"/>
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−            <param name="t" value="1"/>
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−            <output name="output1" file="ath_miRNAs_predicted_targets.txt" compare="contains"/>
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−        </test>
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−    </tests>
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−    <help><![CDATA[
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−**What it does**
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−
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−TargetFinder will computationally predict small RNA binding sites on target transcripts from a sequence database.
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−
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−This is done by aligning the input small RNA sequence against all transcripts,
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−followed by site scoring using a position-weighted scoring matrix.
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−
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−**Input**
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−
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−-f Input small RNA sequences file (FASTA-format).
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−
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−-d Target sequence database file (FASTA-format)
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−
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−**Output**
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−
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−Each predicted target site is printed out separately.
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−The output consists of two parts.
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−
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−The first is a description line and the second is a base-pairing diagram of the target and small RNA (query) sequence.
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−
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−The description line contains the query name, the description line from the target sequence database, and the target prediction score.
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−
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−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.
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−
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−Between the target site sequece and the query sequence are base pair symbols.
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−
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−A ":" (colon) symbol represents an ordinary Watson-Crick base pair, a "." (period) represents a G:U base pair, and a " " (space) represents a mismatch.
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−
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−If a small RNA is predicted to target a sequence more than once, each target site will be output as separate output.
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−]]></help>
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−    <citations>
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−        <citation type="doi">10.1016/j.cell.2005.04.004</citation>
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−        <citation type="doi">10.1371/journal.pone.0000219</citation>
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−        <citation type="doi">10.1007/978-1-60327-005-2_4</citation>
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−    </citations>
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−</tool>
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−