Mercurial > repos > bgruening > dotknot
annotate dotknot.xml @ 0:42d20ff5da1b draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author | bgruening |
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date | Thu, 17 Sep 2015 17:10:07 -0400 |
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42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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1 <tool id="dotknot" name="DotKnot" version="1.3.1"> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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2 <description>pseudoknot prediction in a given RNA sequence</description> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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3 <requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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4 <requirement type="package" version="1.8.5">vienna_rna</requirement> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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5 <requirement type="package" version="1.3.1">dotknot</requirement> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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6 </requirements> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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7 <stdio> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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8 <exit_code range="1:" /> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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9 <exit_code range=":-1" /> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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10 <regex match="Error:" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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11 <regex match="Exception:" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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12 </stdio> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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13 <version_command>dotknot version 1.3.1</version_command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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14 <command><![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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15 cp \$DOTKNOT_ROOT_PATH/* ./ -R && |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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16 dotknot.py |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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17 $input |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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18 $k |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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19 $l |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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20 $g |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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21 > ./output.txt |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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22 #if $g: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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23 && |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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24 mv ./*.ct ./globalstructure.ct |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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25 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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26 ]]></command> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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27 <inputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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28 <param name="input" type="data" format="fasta" label="Upload your FASTA file with RNA sequences:" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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29 help="The FASTA file must contain a comment line starting with > followed by the sequence. |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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30 It can also contain several consecutive sequences and DotKnot will be executed for each sequence in the file."/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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31 |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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32 <param argument="-k" type="boolean" checked="false" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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33 truevalue="-k" falsevalue="" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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34 label="Include kissing hairpins?" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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35 help="Kissing hairpins are complex and biologically relevant types of pseudoknots. |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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36 Inclusion of kissing hairpins will lead to increased run time, |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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37 yet produce more meaningful results."/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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38 |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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39 <param argument="-l" type="boolean" checked="false" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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40 truevalue="-l" falsevalue="" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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41 label="Include near-optimal local pseudoknots?" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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42 help="Shows top five near-optimal local pseudoknots in terms of two criteria: |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
bgruening
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43 estimated free energy to length ratio and lowest estimated free energy. |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
bgruening
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44 This can help to identify promising pseudoknot foldings and may |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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45 compensate for the limitations of the energy parameters."/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
bgruening
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46 |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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47 <param argument="-g" type="boolean" checked="false" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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48 truevalue="-g" falsevalue="" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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49 label="Include global structure?" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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50 help="Shows predicted global structure in addition to predicted pseudoknots."/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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51 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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52 </inputs> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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53 <outputs> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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54 <data name="output" format="txt" from_work_dir="./output.txt" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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55 label="${tool.name} on ${on_string} (output file)"> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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56 </data> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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57 <data name="outfile_globalstructure" format="txt" from_work_dir="./globalstructure.ct" |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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58 label="${tool.name} on ${on_string} (output global structure)"> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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59 <filter>g == True</filter> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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60 </data> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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61 </outputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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62 <tests> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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63 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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64 <param name="input" value="TMV.fasta" ftype="fasta"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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65 <param name="k" value=""/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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66 <param name="l" value=""/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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67 <param name="g" value=""/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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68 <output name="output" file="test1_output.txt" ftype="txt"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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69 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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70 <test> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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71 <param name="input" value="HCoV229E_short_KISSINGHAIRPINS.fasta" ftype="fasta"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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72 <param name="k" value="-k"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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73 <param name="l" value="-l"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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74 <param name="g" value="-g"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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75 <output name="output" file="test2_output.txt" ftype="txt"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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76 <output name="outfile_globalstructure" file="test2_output2.ct" ftype="txt"/> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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77 </test> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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78 </tests> |
42d20ff5da1b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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79 <help><![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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80 |
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81 **WHAT IT DOES** |
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82 |
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83 DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence. |
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84 |
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85 DotKnot extracts stem regions from the secondary structure probability dot plot calculated by RNAfold. Recursive H-type pseudoknots and intramolecular kissing hairpins are constructed and their presence in the sequence is verified. The detected pseudoknots can then be further analysed using bioinformatics or laboratory techniques. |
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86 |
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87 ----- |
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88 |
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89 **INPUT** |
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90 |
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91 The FASTA file must contain a comment line starting with > followed by the sequence. It can also |
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92 contain several consecutive sequences and DotKnot will be executed for each sequence in the file. |
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93 |
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94 Please ensure that only bases A,C,G,U,T (a,c,g,u,t) are used. |
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95 |
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96 *Example*:: |
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97 |
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98 > Arc-Ful-SRP short |
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99 GGGGGGUUCGGCGUCCCCUGUAACCCGAAACCGCCGAUACGCGGG |
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100 > MMTV |
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101 AAAAAACUUGUAAAGGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAUG |
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102 |
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103 ----- |
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104 |
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105 **OPTIONAL ARGUMENTS** |
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106 |
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107 *Kissing hairpins*:: |
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108 Kissing hairpins are complex and biologically relevant types of pseudoknots. |
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109 Inclusion of kissing hairpins will lead to increased run time, yet produce more meaningful |
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110 results. |
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111 |
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112 *local pseudoknots*:: |
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113 Shows top five near-optimal local pseudoknots in terms of two criteria: estimated free energy |
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114 to length ratio and lowest estimated free energy. This can help to identify promising pseudoknot |
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115 foldings and may compensate for the limitations of the energy parameters. |
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116 *global structure*:: |
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117 Shows predicted global structure in addition to predicted pseudoknots |
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118 |
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119 ----- |
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120 |
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121 **OUTPUT** |
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122 |
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123 Each pseudoknot is displayed in dot-bracket notation. Unpaired bases are indicated by dots. Base |
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124 pairs are written as bracket pairs. The first stem of a pseudoknot is indicated by round brackets , i.e. ( and ). The second stem of a pseudoknot is indicated by square brackets, i.e. [ and ]. |
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125 |
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126 We also give the start and end positions of the pseudoknot with respect to the input sequence. If the global structure option is chosen (-g:), a CT file will be created which contains the global |
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127 structure. The file name will start with the identifier given in the FASTA file. |
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128 |
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129 ----- |
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130 |
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131 **dotknot** is a Free and Open Source Software, see more details and background information on the dotknot dotknot_ Website. |
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132 |
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133 .. _dotknot: http://dotknot.csse.uwa.edu.au/ |
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134 |
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135 ]]></help> |
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136 <citations> |
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137 <citation type="doi">10.1093/nar/gkq021</citation> |
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138 <citation type="doi">10.1261/rna.2394511</citation> |
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139 </citations> |
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140 </tool> |