Mercurial > repos > rnateam > viennarna_rnacofold
changeset 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 | af146690a82f |
| children | 93c94bf87a04 |
| files | rnacofold.xml |
| diffstat | 1 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/rnacofold.xml Tue Jul 18 01:47:42 2017 -0400 +++ b/rnacofold.xml Fri Sep 22 15:56:00 2017 -0400 @@ -28,6 +28,9 @@ $constraints.constraintLocation.canonicalBPonly $constraints.constraintLocation.enforceConstraint #end if + #if str($constraints.constraintLocation.constraintSelector) == "inFile" + -C + #end if $algorithm_options.allpf #if len($algorithm_options.concfiles) == 1 #for $i in $algorithm_options.concfiles @@ -107,14 +110,16 @@ <section name="constraints" title="Structure constraints"> <conditional name="constraintLocation"> <param name="constraintSelector" type="select" label="Constraints"> - <!-- <option value="fromInput">The constraints are included in the input file</option> --> + <!-- <option value="fromInput">The constraints are included in the input file</option> --> <option value="fromFile">The constraints are in a seperate file</option> + <option value="inFile">The constraints are in the fasta input file</option> <option value="none" selected="true">Don't use constraints</option> </param> <!-- <when value="fromInput"></when> --> <when value="none"></when> + <when value="inFile"></when> <when value="fromFile"> - <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/> + <param name="constraintsFile" type="data" format="txt" label="Constraints file" argument="--constraint"/> <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" /> <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" /> </when> @@ -129,7 +134,7 @@ <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"/> <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)."/> <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"> - <param type="data" name="concfile" format="*" label="Concentrations file"/> + <param type="data" name="concfile" format="txt" label="Concentrations file"/> </repeat> <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."/> <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."/>