Mercurial > repos > rnateam > viennarna_rnafold

comparison rnafold.xml @ 3:fcf2463f85c1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 04c9cc19a39fea2e20986ca27d364f86f65184fd
author rnateam
date Mon, 29 May 2017 17:24:36 -0400
parents 84aad99aca1f
children b31dcdb31209
comparison
equal deleted inserted replaced
2:84aad99aca1f 3:fcf2463f85c1
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&lt;designation&gt;.+)_ss\.ps" ext="eps" /> 293 <discover_datasets pattern="(?P&lt;designation&gt;.+)_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&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/> 297 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>