Mercurial > repos > rnateam > viennarna_rnafold
comparison rnafold.xml @ 3:fcf2463f85c1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 04c9cc19a39fea2e20986ca27d364f86f65184fd
author | rnateam |
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date | Mon, 29 May 2017 17:24:36 -0400 |
parents | 84aad99aca1f |
children | b31dcdb31209 |
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2:84aad99aca1f | 3:fcf2463f85c1 |
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1 <tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.1"> | 1 <tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.2"> |
2 <description>Calculate minimum free energy secondary structures and partition function of RNAs</description> | 2 <description>Calculate minimum free energy secondary structures and partition function of RNAs</description> |
3 <macros> | 3 <macros> |
4 <token name="@EXECUTABLE@">RNAfold</token> | 4 <token name="@EXECUTABLE@">RNAfold</token> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
43 #end if | 43 #end if |
44 #end if | 44 #end if |
45 $advancedOptions.noconversion | 45 $advancedOptions.noconversion |
46 $advancedOptions.gquad | 46 $advancedOptions.gquad |
47 $advancedOptions.nolp | 47 $advancedOptions.nolp |
48 $advancedOptions.nops | |
48 $advancedOptions.nogu | 49 $advancedOptions.nogu |
49 $advancedOptions.noclosinggu | 50 $advancedOptions.noclosinggu |
50 $advancedOptions.notetra | 51 $advancedOptions.notetra |
51 $advancedOptions.circular | 52 $advancedOptions.circular |
52 #if $advancedOptions.bppmThreshold <> 1e-5 | 53 #if $advancedOptions.bppmThreshold <> 1e-5 |
146 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/> | 147 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/> |
147 <param argument="--pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/> | 148 <param argument="--pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/> |
148 </when> | 149 </when> |
149 </conditional> | 150 </conditional> |
150 <section name="advancedOptions" title="Advanced options"> | 151 <section name="advancedOptions" title="Advanced options"> |
152 <param name="nops" type="boolean" truevalue="--noPS" falsevalue="" checked="false" label="Do not produce postscript drawing of the mfe structure (reduces run-time)" help="(--noPS)"/> | |
151 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/> | 153 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/> |
152 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/> | 154 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/> |
153 <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"/> | 155 <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"/> |
154 <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)"/> | 156 <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)"/> |
155 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/> | 157 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/> |
212 <param name="shapeSelector" type="select" label="Shape reactivity data"> | 214 <param name="shapeSelector" type="select" label="Shape reactivity data"> |
213 <option value="isUsed">Use shape reactivity data</option> | 215 <option value="isUsed">Use shape reactivity data</option> |
214 <option value="notUsed" selected="true">Don't use shape reactivity data</option> | 216 <option value="notUsed" selected="true">Don't use shape reactivity data</option> |
215 </param> | 217 </param> |
216 <when value ="isUsed"> | 218 <when value ="isUsed"> |
217 <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/> | 219 <param type="data" name="shapeFile" format="txt" label="Shape file" argument="--shape"/> |
218 <conditional name="shapeMethod"> | 220 <conditional name="shapeMethod"> |
219 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod"> | 221 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod"> |
220 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option> | 222 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option> |
221 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option> | 223 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option> |
222 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option> | 224 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option> |
285 </section> | 287 </section> |
286 </inputs> | 288 </inputs> |
287 <outputs> | 289 <outputs> |
288 <data format="dbn" name="tabular_file"/> | 290 <data format="dbn" name="tabular_file"/> |
289 <collection name="sequence_outputs" type="list" label="rna_eps outputs"> | 291 <collection name="sequence_outputs" type="list" label="rna_eps outputs"> |
292 <filter>advancedOptions['nops'] is False</filter> | |
290 <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" /> | 293 <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" /> |
291 </collection> | 294 </collection> |
292 <collection name="matrix_outputs" type="list" label="rna_eps outputs"> | 295 <collection name="matrix_outputs" type="list" label="rna_eps outputs"> |
293 <filter>measelect['pf'] is True</filter> | 296 <filter>measelect['pf'] is True</filter> |
294 <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> | 297 <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> |