Mercurial > repos > rnateam > viennarna_rnacofold
comparison rnacofold.xml @ 5:73747fe9e88b 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 15:56:00 -0400 |
| parents | cb8201484ad8 |
| children |
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| 4:af146690a82f | 5:73747fe9e88b |
|---|---|
| 25 #end if | 25 #end if |
| 26 #if str($constraints.constraintLocation.constraintSelector) == "fromFile" | 26 #if str($constraints.constraintLocation.constraintSelector) == "fromFile" |
| 27 --constraint='$constraints.constraintLocation.constraintsFile' | 27 --constraint='$constraints.constraintLocation.constraintsFile' |
| 28 $constraints.constraintLocation.canonicalBPonly | 28 $constraints.constraintLocation.canonicalBPonly |
| 29 $constraints.constraintLocation.enforceConstraint | 29 $constraints.constraintLocation.enforceConstraint |
| 30 #end if | |
| 31 #if str($constraints.constraintLocation.constraintSelector) == "inFile" | |
| 32 -C | |
| 30 #end if | 33 #end if |
| 31 $algorithm_options.allpf | 34 $algorithm_options.allpf |
| 32 #if len($algorithm_options.concfiles) == 1 | 35 #if len($algorithm_options.concfiles) == 1 |
| 33 #for $i in $algorithm_options.concfiles | 36 #for $i in $algorithm_options.concfiles |
| 34 --concfile='$i.concfile' | 37 --concfile='$i.concfile' |
| 105 argument="--betaScale"/> | 108 argument="--betaScale"/> |
| 106 </section> | 109 </section> |
| 107 <section name="constraints" title="Structure constraints"> | 110 <section name="constraints" title="Structure constraints"> |
| 108 <conditional name="constraintLocation"> | 111 <conditional name="constraintLocation"> |
| 109 <param name="constraintSelector" type="select" label="Constraints"> | 112 <param name="constraintSelector" type="select" label="Constraints"> |
| 110 <!-- <option value="fromInput">The constraints are included in the input file</option> --> | 113 <!-- <option value="fromInput">The constraints are included in the input file</option> --> |
| 111 <option value="fromFile">The constraints are in a seperate file</option> | 114 <option value="fromFile">The constraints are in a seperate file</option> |
| 115 <option value="inFile">The constraints are in the fasta input file</option> | |
| 112 <option value="none" selected="true">Don't use constraints</option> | 116 <option value="none" selected="true">Don't use constraints</option> |
| 113 </param> | 117 </param> |
| 114 <!-- <when value="fromInput"></when> --> | 118 <!-- <when value="fromInput"></when> --> |
| 115 <when value="none"></when> | 119 <when value="none"></when> |
| 120 <when value="inFile"></when> | |
| 116 <when value="fromFile"> | 121 <when value="fromFile"> |
| 117 <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/> | 122 <param name="constraintsFile" type="data" format="txt" label="Constraints file" argument="--constraint"/> |
| 118 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" /> | 123 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" /> |
| 119 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" /> | 124 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" /> |
| 120 </when> | 125 </when> |
| 121 </conditional> | 126 </conditional> |
| 122 </section> | 127 </section> |
| 127 <option value="1" >1: Calculate the partition function and base pairing probability matrix</option> | 132 <option value="1" >1: Calculate the partition function and base pairing probability matrix</option> |
| 128 </param> | 133 </param> |
| 129 <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers as well as A and B monomers" help="--all_pf"/> | 134 <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers as well as A and B monomers" help="--all_pf"/> |
| 130 <param argument="-c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Concentrations" help="In addition to everything listed under the -a option, read in initial monomer concentrations and compute the expected equilibrium concentrations of the 5 possible species (AB, AA, BB, A, B)."/> | 135 <param argument="-c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Concentrations" help="In addition to everything listed under the -a option, read in initial monomer concentrations and compute the expected equilibrium concentrations of the 5 possible species (AB, AA, BB, A, B)."/> |
| 131 <repeat name="concfiles" title="A file with initial concentrations for the two sequences" default="0" max="1" help="The table consits of arbitrary many lines with just two numbers (the concentration of sequence A and B). This option will automatically toggle the −c (and thus -a and --all_pf) options"> | 136 <repeat name="concfiles" title="A file with initial concentrations for the two sequences" default="0" max="1" help="The table consits of arbitrary many lines with just two numbers (the concentration of sequence A and B). This option will automatically toggle the −c (and thus -a and --all_pf) options"> |
| 132 <param type="data" name="concfile" format="*" label="Concentrations file"/> | 137 <param type="data" name="concfile" format="txt" label="Concentrations file"/> |
| 133 </repeat> | 138 </repeat> |
| 134 <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."/> | 139 <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."/> |
| 135 <param argument="--bppmThreshold" type="float" value="1e-5" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data."/> | 140 <param argument="--bppmThreshold" type="float" value="1e-5" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data."/> |
| 136 <param argument="--gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="take into account G Quadruplex formation"/> | 141 <param argument="--gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="take into account G Quadruplex formation"/> |
| 137 </section> | 142 </section> |