comparison iqtree.xml @ 18:f87ac61981f0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490

17:0878b7fd5260

$bootstrap_parameters.nonparametric_bootstrap.tbe

#if str($miscellaneous_options.fconst) != ''
    -fconst '$miscellaneous_options.fconst'
#end if
]]>
    </command>
    <inputs>
        <section name="general_options" expanded="true" title="General options">
            <param argument="-s" type="data" format="txt,fasta,phylip,nex,clustal,msf" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>

        <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
            <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
                <expand macro="sanitize_query"
                validinitial="string.digits,string.punctuation" />
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
        <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />

18:f87ac61981f0

$bootstrap_parameters.nonparametric_bootstrap.tbe

#if str($miscellaneous_options.fconst) != ''
    -fconst '$miscellaneous_options.fconst'
#end if

#if str($miscellaneous_options.blmin) != ''
    -blmin $miscellaneous_options.blmin
#end if

#if str($miscellaneous_options.blmax) != ''
    -blmax $miscellaneous_options.blmax
#end if

]]>
    </command>
    <inputs>
        <section name="general_options" expanded="true" title="General options">
            <param argument="-s" type="data" format="txt,fasta,phylip,nex,clustal,msf" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>

        <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
            <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
                <expand macro="sanitize_query"
                validinitial="string.digits,string.punctuation" />
            </param>
            <param argument="-blmin" type="float" min="0" max="1" value="" optional="true" label="Specify minimum branch length" help="Default: the smaller of 0.000001 and 0.1/alignment_length." />
            <param argument="-blmax" type="float" min="0" max="1" value="" optional="true" label="Specify the maximum branch length" help="Default: 10" />
        </section>
    </inputs>
    <outputs>
        <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
        <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />