Mercurial > repos > rnateam > viennarna_rnacofold

comparison rnacofold.xml @ 1:cb8201484ad8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 14f0b39f64982773ef0367379b915f742eabcc1b
author rnateam
date Wed, 21 Dec 2016 17:32:46 -0500
parents f3d4656ed57c
children 73747fe9e88b
comparison
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0:f3d4656ed57c 1:cb8201484ad8
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"/> 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"/>
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)."/> 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)."/>
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"> 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">
132 <param type="data" name="concfile" format="*" label="Concentrations file"/> 132 <param type="data" name="concfile" format="*" label="Concentrations file"/>
133 </repeat> 133 </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." argumen="--pfScale"/> 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."/>
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." argumen="--bppmThreshold"/> 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."/>
136 <param argument="--gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="take into account G Quadruplex formation"/> 136 <param argument="--gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="take into account G Quadruplex formation"/>
137 </section> 137 </section>
138 </inputs> 138 </inputs>
139 <outputs> 139 <outputs>
140 <data format="txt" name="tabularFile"/> 140 <data format="txt" name="tabularFile"/>