comparison rnafold.xml @ 6:b31dcdb31209 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty

5:b05424042661

                    </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="batch" type="boolean" checked="false" truevalue="--batch" falsevalue=""
                            label="Use constraints for all alignment records"
                            help="Usually, constraints provided from input file are only applied to a single sequence alignment. Therefore, RNAalifold will stop its computation and quit after the first input alignment was processed. Using this switch, RNAfold processes all sequence alignments in the input and applies the same provided constraints to each of them."
                            argument="--batch"/>
                        <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" />

                            </conditional>
                        </when>
                        <when value="notUsed">
                        </when>
                </conditional>
                <param argument="--motif" type="text" value="" label="Sequence structure energy" help="Specify stabilizing effect of ligand binding to a particular sequence/structure motif. Some ligands binding to RNAs require and/or induce particular sequence and structure motifs. For instance they bind to an interior loop, or small hairpin loop. If for such cases a binding free energy is known, the binding and therefore stabilizing effect of the ligand can be included in the folding recursions. Interior loop motifs are specified as concatenations of 5’ and 3’ motif, separated by an ’&amp;’ character. Energy contributions must be specified in kcal/mol."/>
        </section>
        <section name="IDs" title="Naming Conventions">
            <param name="auto_id"
                type="boolean" truevalue="--auto-id" falsevalue="" checked="false"
                label="Automatically generate an ID for each alignment."

6:b31dcdb31209

                    </param>
                <!--	<when value="fromInput"></when> -->
                <when value="none"></when>
		<when value="inFile"></when>
                    <when value="fromFile">
                        <param name="constraintsFile" type="data" format="txt" label="Constraints file" argument="--constraint"/>
                        <param name="batch" type="boolean" checked="false" truevalue="--batch" falsevalue=""
                            label="Use constraints for all alignment records"
                            help="Usually, constraints provided from input file are only applied to a single sequence alignment. Therefore, RNAalifold will stop its computation and quit after the first input alignment was processed. Using this switch, RNAfold processes all sequence alignments in the input and applies the same provided constraints to each of them."
                            argument="--batch"/>
                        <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" />

                            </conditional>
                        </when>
                        <when value="notUsed">
                        </when>
                </conditional>
                <param argument="--motif" type="text" value="" label="Sequence structure energy" help="Specify stabilizing effect of ligand binding to a particular sequence/structure motif. Some ligands binding to RNAs require and/or induce particular sequence and structure motifs. For instance they bind to an interior loop, or small hairpin loop. If for such cases a binding free energy is known, the binding and therefore stabilizing effect of the ligand can be included in the folding recursions. Interior loop motifs are specified as concatenations of 5’ and 3’ motif, separated by an ’&amp;’ character. Energy contributions must be specified in kcal/mol.">
                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
				</param>
        </section>
        <section name="IDs" title="Naming Conventions">
            <param name="auto_id"
                type="boolean" truevalue="--auto-id" falsevalue="" checked="false"
                label="Automatically generate an ID for each alignment."