Mercurial > repos > rnateam > viennarna_rnasubopt

comparison rnasubopt.xml @ 5:685d5971df5b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty
author rnateam
date Fri, 22 Sep 2017 15:59:40 -0400
parents 58fe85fe08be
children
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4:19ddab671d92 5:685d5971df5b
133 <option value="none" selected="true">Don't use constraints</option> 133 <option value="none" selected="true">Don't use constraints</option>
134 </param> 134 </param>
135 <!-- <when value="fromInput"></when> --> 135 <!-- <when value="fromInput"></when> -->
136 <when value="none"></when> 136 <when value="none"></when>
137 <when value="fromFile"> 137 <when value="fromFile">
138 <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/> 138 <param name="constraintsFile" type="data" format="txt" label="Constraints file" argument="--constraint"/>
139 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from the structure constraint" /> 139 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from the structure constraint" />
140 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" /> 140 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
141 </when> 141 </when>
142 </conditional> 142 </conditional>
143 143
145 <param name="shapeSelector" type="select" label="Shape reactivity data"> 145 <param name="shapeSelector" type="select" label="Shape reactivity data">
146 <option value="isUsed">Use shape reactivity data</option> 146 <option value="isUsed">Use shape reactivity data</option>
147 <option value="notUsed" selected="true">Don't use shape reactivity data</option> 147 <option value="notUsed" selected="true">Don't use shape reactivity data</option>
148 </param> 148 </param>
149 <when value ="isUsed"> 149 <when value ="isUsed">
150 <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/> 150 <param type="data" name="shapeFile" format="txt" label="Shape file" argument="--shape"/>
151 <conditional name="shapeMethod"> 151 <conditional name="shapeMethod">
152 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod"> 152 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod">
153 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option> 153 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option>
154 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option> 154 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option>
155 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option> 155 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option>