comparison rnafold.xml @ 1:f87325531be8 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 14f0b39f64982773ef0367379b915f742eabcc1b

0:d6044fad075f

    #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
        --constraint='$constraints.constraintLocation.constraintsFile'
        $constraints.constraintLocation.batch
        $constraints.constraintLocation.canonicalBPonly
        $constraints.constraintLocation.enforceConstraint
    #end if
    #if str($constraints.shapeOption.shapeSelector) == "isUsed"
        --shape='$constraints.shapeOption.shapeFile'
        #if str($constraints.shapeOption.shapeMethod.methodSelector) == "W"
            #set $s="W"

                <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
                <conditional name="constraintLocation">
                    <param name="constraintSelector" type="select" label="Constraints">
                        <!-- <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="none" selected="true">Don't use constraints</option>
                    </param>
                <!--	<when value="fromInput"></when> -->
                    <when value="none"></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, RNAalifold 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" />
                        <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
                    </when>
                </conditional>						

        </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." 
                help="If this flag is active, RNAalifold ignores any IDs retrieved from the input and automatically generates an ID for each alignment." 
                argument="--auto-id"/>
            <param name="id_prefix" 
                type="text" value="alignment" 
                label="Prefix for automatically generated IDs (as used in output file names)" 
                help="If this parameter is set, each alignment will be prefixed with the provided string. Hence, the output files will obey the following naming scheme: 'prefix_xxxx_ss.ps' (secondary structure plot), 'prefix_xxxx_dp.ps' (dot−plot), 'prefix_xxxx_aln.ps' (annotated alignment), etc. where xxxx is the alignment number beginning with the second alignment in the input. Use this setting in conjunction with the −−continuous−ids flag to assign IDs beginning with the first input alignment." 
                argument="--id-prefix"/>
            <param name="id_digits" 
                type="integer" value="4" min="1" max="18" 
                label="The number of digits of the counter in automatically generated alignment IDs" 
                help="When alignments IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left−padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]." 
                argument="--id-digits"/>
            <param name="id_start" 
                type="integer" value="1" min="0" 
                label="First number in automatically generated alignment IDs" 
                help="When alignment IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous alignment IDs, i.e. it activates the −−continuous−ids flag.." 
                argument="--id-start"/>
        </section>        
    </inputs>
    <outputs>
        <data format="dbn" name="tabular_file"/>

1:f87325531be8

    #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
        --constraint='$constraints.constraintLocation.constraintsFile'
        $constraints.constraintLocation.batch
        $constraints.constraintLocation.canonicalBPonly
        $constraints.constraintLocation.enforceConstraint
    #end if
    #if str($constraints.constraintLocation.constraintSelector) == "inFile"
        -C
    #end if
    #if str($constraints.shapeOption.shapeSelector) == "isUsed"
        --shape='$constraints.shapeOption.shapeFile'
        #if str($constraints.shapeOption.shapeMethod.methodSelector) == "W"
            #set $s="W"

                <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
                <conditional name="constraintLocation">
                    <param name="constraintSelector" type="select" label="Constraints">
                        <!-- <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="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" />
                        <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
                    </when>
                </conditional>						

        </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." 
                help="If this flag is active, RNAfold ignores any IDs retrieved from the input and automatically generates an ID for each sequence." 
                argument="--auto-id"/>
            <param name="id_prefix" 
                type="text" value="sequence" 
                label="Prefix for automatically generated IDs (as used in output file names)" 
                help="If this parameter is set, each sequence will be prefixed with the provided string. Hence, the output files will obey the following naming scheme: 'prefix_xxxx_ss.ps' (secondary structure plot), 'prefix_xxxx_dp.ps' (dot−plot), 'prefix_xxxx_aln.ps' (annotated sequence), etc. where xxxx is the sequence number beginning with the second sequence in the input. Use this setting in conjunction with the −−continuous−ids flag to assign IDs beginning with the first input sequence." 
                argument="--id-prefix"/>
            <param name="id_digits" 
                type="integer" value="4" min="1" max="18" 
                label="The number of digits of the counter in automatically generated sequence IDs" 
                help="When sequences IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left−padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]." 
                argument="--id-digits"/>
            <param name="id_start" 
                type="integer" value="1" min="0" 
                label="First number in automatically generated sequence IDs" 
                help="When sequence IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous sequence IDs, i.e. it activates the −−continuous−ids flag.." 
                argument="--id-start"/>
        </section>        
    </inputs>
    <outputs>
        <data format="dbn" name="tabular_file"/>