Mercurial > repos > rnateam > viennarna_rnasubopt
comparison rnasubopt.xml @ 5:685d5971df5b draft
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> |