Mercurial > repos > bgruening > viennarna_rnaup
annotate rnaup.xml @ 0:2c27f1137818 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
| author | bgruening |
|---|---|
| date | Wed, 05 Oct 2016 11:53:02 -0400 |
| parents | |
| children |
| rev | line source |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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1 <tool id="viennarna_rnaup" name="@EXECUTABLE@" version="@VERSION@.0"> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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2 <description>Calculate the thermodynamics of RNA-RNA interactions</description> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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3 <macros> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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4 <token name="@EXECUTABLE@">RNAup</token> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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5 <import>macros.xml</import> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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6 </macros> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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7 <expand macro="requirements" /> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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8 <expand macro="stdio" /> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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9 <expand macro="version_command" /> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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10 <command> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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11 <![CDATA[ |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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12 RNAup < '$input' > '$output' |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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13 -T$temperature |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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14 --dangles=$dangling |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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15 $constraint |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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16 --ulength=$ulength |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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17 --contributions=#echo ''.join(str($contributions).split(','))# |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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18 --window=$window |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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19 $includeboth |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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20 $interactionpairwise |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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21 $interactionfirst |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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22 --extend5=$extendfive |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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23 --extend3=$extendthree |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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24 #if $varExists('$advancedOptions.nolp') |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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25 --pfScale=$advancedOptions.pfscale |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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26 $advancedOptions.noconversion |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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27 $advancedOptions.nolp |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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28 $advancedOptions.nogu |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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29 $advancedOptions.noclosinggu |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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30 $advancedOptions.notetra |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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31 #end if |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
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32 && tar -cf '$accesibilitiesFile' *.out |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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33 ]]> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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34 </command> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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35 |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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changeset
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36 <inputs> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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37 <param format="fasta" name="input" type="data" label="Fasta file"/> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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39 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d"> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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40 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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41 <option value="0">ignore dangling ends (0)</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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42 <option value="1">unpaired bases participate in one dangling end only (1)</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
parents:
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43 <option value="3">allow coaxial stacking (3)</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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parents:
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44 </param> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
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48 <option value="S" selected="true">sum of all</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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49 <option value="H">unpaired within hairpin loop</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
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50 <option value="I">unpaired within interior loop</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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51 <option value="M">unpaired within multiloop</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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52 <option value="E">unpaired within exterior loop</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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53 <validator type="no_options" message="Please select at least one contribution."/> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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parents:
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54 </param> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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61 <conditional name="advancedOptions"> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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62 <param name="advancedSelector" type="select" label="advanced options"> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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63 <option value="basic">basic Options</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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64 <option value="advanced">advanced Options</option> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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65 </param> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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66 <when value="advanced"> |
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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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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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2c27f1137818
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
bgruening
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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> |