Mercurial > repos > rnateam > targetfinder
annotate TargetFinder.xml @ 0:773fdd1a02ea draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
author | rnateam |
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date | Wed, 21 Dec 2016 17:31:28 -0500 |
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children | c9d56748fbde |
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773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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1 <tool id="targetfinder" name="Plant small RNA target prediction tool" version="1.7.0"> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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2 <requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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3 <requirement type="package" version="1.7">targetfinder</requirement> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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4 </requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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5 <stdio> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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6 <exit_code range="1:" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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7 </stdio> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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8 <command><![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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9 targetfinder_threads.pl |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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10 -f $f |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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11 -d $d |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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12 -c $c |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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13 -t "\${GALAXY_SLOTS:-12}" |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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14 $r |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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15 -o $output1 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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16 ]]></command> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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17 <inputs> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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18 <param label="Input small RNA sequences file" help="(-f) FASTA-format" name="f" type="data" format="fasta" /> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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19 <param label="Target sequence database file" help="(-d) FASTA-format" name="d" type="data" format="fasta" /> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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20 <param label="Prediction score cutoff value" help="(-c) DEFAULT = 4" name="c" type="float" value="4.0" /> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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21 <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" /> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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22 </inputs> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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23 <outputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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24 <data name="output1" format="data"/> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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25 </outputs> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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26 <tests> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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27 <test> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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28 <param name="f" value="ath_miRNAs_test.fa"/> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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29 <param name="d" value="Antirrhinum_majus.mRNA.EST.fasta"/> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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30 <param name="r" value=""/> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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31 <param name="c" value="4.0"/> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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32 <param name="t" value="1"/> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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33 <output name="output1" file="ath_miRNAs_predicted_targets.txt" compare="contains"/> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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34 </test> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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35 </tests> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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36 <help><![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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37 **What it does** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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38 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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39 TargetFinder will computationally predict small RNA binding sites on target transcripts from a sequence database. |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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40 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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41 This is done by aligning the input small RNA sequence against all transcripts, |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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42 followed by site scoring using a position-weighted scoring matrix. |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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43 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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44 **Input** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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45 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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46 -f Input small RNA sequences file (FASTA-format). |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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47 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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48 -d Target sequence database file (FASTA-format) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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49 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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50 **Output** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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51 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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52 Each predicted target site is printed out separately. |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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53 The output consists of two parts. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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54 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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55 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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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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56 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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57 The description line contains the query name, the description line from the target sequence database, and the target prediction score. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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58 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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59 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. |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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60 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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61 Between the target site sequece and the query sequence are base pair symbols. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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62 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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63 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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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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64 |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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65 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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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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66 ]]></help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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67 <citations> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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68 <citation type="doi">10.1016/j.cell.2005.04.004</citation> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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69 <citation type="doi">10.1371/journal.pone.0000219</citation> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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70 <citation type="doi">10.1007/978-1-60327-005-2_4</citation> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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71 </citations> |
773fdd1a02ea
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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72 </tool> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
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73 |