Mercurial > repos > rnateam > viennarna_rnaup
annotate rnaup.xml @ 6:0a840ecbd627 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
| author | rnateam |
|---|---|
| date | Wed, 20 Dec 2017 08:34:12 -0500 |
| parents | d14bc79748a3 |
| children |
| rev | line source |
|---|---|
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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changeset
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1 <tool id="viennarna_rnaup" name="@EXECUTABLE@" version="@VERSION@.0"> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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2 <description>Calculate the thermodynamics of RNA-RNA interactions</description> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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3 <macros> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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4 <token name="@EXECUTABLE@">RNAup</token> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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5 <import>macros.xml</import> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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6 </macros> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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changeset
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7 <expand macro="requirements" /> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
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8 <expand macro="stdio" /> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
changeset
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9 <expand macro="version_command" /> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
changeset
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10 <command> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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11 <![CDATA[ |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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12 RNAup < '$input' > '$output' |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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13 -T$temperature |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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14 --dangles=$dangling |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
changeset
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15 $constraint |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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16 --ulength=$ulength |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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17 --contributions=#echo ''.join(str($contributions).split(','))# |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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18 --window=$window |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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19 $includeboth |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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changeset
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20 $interactionpairwise |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
changeset
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21 $interactionfirst |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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22 --extend5=$extendfive |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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23 --extend3=$extendthree |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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24 #if $varExists('$advancedOptions.nolp') |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
changeset
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25 --pfScale=$advancedOptions.pfscale |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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26 $advancedOptions.noconversion |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
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27 $advancedOptions.nolp |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
diff
changeset
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28 $advancedOptions.nogu |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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29 $advancedOptions.noclosinggu |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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30 $advancedOptions.notetra |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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31 #end if |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
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32 && tar -cf '$accesibilitiesFile' *.out |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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33 ]]> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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34 </command> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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35 |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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36 <inputs> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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37 <param format="fasta" name="input" type="data" label="Fasta file"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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changeset
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38 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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39 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d"> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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40 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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41 <option value="0">ignore dangling ends (0)</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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42 <option value="1">unpaired bases participate in one dangling end only (1)</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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43 <option value="3">allow coaxial stacking (3)</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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44 </param> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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45 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Constraints for the secondary structure" help="--constraint"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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46 <param name="ulength" type="integer" min="0" value="4" label="Length of the unstructured region." help="--ulength"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
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47 <param name="contributions" type="select" multiple="true" display="checkboxes" label="Specify which contributions to the probabilty of being unpaired are listed in the output" argument="--contributions"> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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48 <option value="S" selected="true">sum of all</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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49 <option value="H">unpaired within hairpin loop</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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50 <option value="I">unpaired within interior loop</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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51 <option value="M">unpaired within multiloop</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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52 <option value="E">unpaired within exterior loop</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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53 <validator type="no_options" message="Please select at least one contribution."/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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54 </param> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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55 <param name="window" type="integer" min="0" value="25" label="Maximal length of the region of interaction." help="--window"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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56 <param name="includeboth" type="boolean" truevalue="--include_both" falsevalue="" checked="false" label="Include the probability of unpaired regions in both RNAs" help="--include_both"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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57 <param name="interactionpairwise" type="boolean" truevalue="--interaction_pairwise" falsevalue="" checked="false" label="Activate pairwise interaction mode" help="--interaction_pairwise"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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58 <param name="interactionfirst" type="boolean" truevalue="--interaction_first" falsevalue="" checked="false" label="Activate pairwise interaction mode, compare always with the first sequence" help="--interaction_first"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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59 <param name="extendfive" type="integer" min="0" value="0" label="Extend the region of interaction in the target to some residues on the 5' side." help="--extend5"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
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60 <param name="extendthree" type="integer" min="0" value="0" label="Extend the region of interaction in the target to some residues on the 3' side." help="--extend3"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
parents:
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61 <conditional name="advancedOptions"> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
rnateam
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62 <param name="advancedSelector" type="select" label="advanced options"> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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63 <option value="basic">basic Options</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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64 <option value="advanced">advanced Options</option> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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65 </param> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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66 <when value="advanced"> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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67 <param name="pfscale" type="float" value="1.07" label="Use scale*mfe as an estimate for the ensemble free energy " help="--pfScale"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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68 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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69 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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70 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/> |
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d14bc79748a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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71 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/> |
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72 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/> |
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73 </when> |
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74 <when value="basic"> |
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75 </when> |
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76 </conditional> |
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77 </inputs> |
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78 <outputs> |
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79 <data format="txt" name="output"/> |
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80 <data format="tar" name="accesibilitiesFile"/> |
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81 </outputs> |
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82 <tests> |
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83 <test> |
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84 <param name="input" value="rnaup_input1.fa"/> |
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85 <output name="output" file="rnaup_result1.txt"/> |
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86 </test> |
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87 </tests> |
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88 <help> |
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89 <![CDATA[ |
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90 |
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91 **RNAup** |
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92 |
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93 RNAup calculates the thermodynamics of RNA−RNA interactions, by decomposing the binding into two stages. (1) First the probability that a potential binding sites remains unpaired (equivalent to the free energy needed to open the site) is computed. (2) Then this accessibility is combined with the interaction energy to obtain the total binding energy. All calculations are done by computing partition functions over all possible conformations. |
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94 |
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95 RNAup provides two different modes: By default RNAup computes accessibilities, in terms of the free energies needed to open a region (default length 4). It prints the region of highest accessibility and its opening energy to stdout, opening energies for all other regions are written to a file. |
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96 |
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97 In interaction mode the interaction between two RNAs is calculated. It is invoked if the input consists of two sequences concatenated with an "&". RNAup assumes that the longer RNA is a structured target sequence while the shorter one is an unstructured small RNA. Additionally, for every position along the target sequence the best free energy of binding for an interaction that includes this position is written to the the output file. Output to stdout consists of the location and free energy, dG, for the optimal region of interaction. The binding energy dG is also split into its components the interaction energy dGint and the opening energy dGu_l (and possibly dGu_s for the shorter sequence). |
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98 In addition we print the optimal interaction structure as computed by RNAduplex for this region. Note that it can happen that the RNAduplex computed optimal interaction does not coincide with the optimal RNAup region. If the two predictions don’t match the structure string is replaced by a run of ".". |
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99 |
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100 ----- |
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101 |
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102 **Input format** |
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103 |
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104 RNAup requires one input file |
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105 |
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106 - Fasta file |
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107 |
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108 For the interaction mode, the sequences of the query and target have to be concatenated by an '&', or the --interaction-pairwise or --interaction-first flags have to be set. |
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109 |
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110 ------ |
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111 |
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112 **Outputs** |
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113 |
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114 - most accesible region of each sequence |
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115 - accesibilties of each sequence is written in a file and these files are bundled together in a tar file |
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116 |
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117 |
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118 ]]> |
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119 </help> |
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120 <expand macro="citations" /> |
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121 </tool> |