comparison iqtree.xml @ 8:c1d53e95327f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563"

7:524d31add34a

#end if

## date options
#if str($time_tree.date_source.select_source) == 'dataset':
    #if $time_tree.date_source.date:
        --date $time_tree.date_source.date
    #end if
#elif str($time_tree.date_source.select_source) == 'input':
    --date TAXNAME
    #if str($time_tree.date_source.date_tip) != '':
        --date-tip '$time_tree.date_source.date_tip'

#end if
]]>
    </command>
    <inputs>
        <section name="general_options" expanded="true" title="General options">
            <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
            <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output">
                <expand macro="sanitize_query" />
            </param>

            <param type="boolean" name="short_alignments" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." />

                    <option value="input">Derive from input</option>
                </param>
                <when value="none" />
                <when value="input" />
                <when value="dataset">
                    <param argument="--date" type="data" format="text" optional="true" label="File containing dates of tips or ancestral nodes" />
                </when>
            </conditional>
            <param argument="--date-tip" type="text" optional="true" label="Tip dates as a real number or YYYY-MM-DD">
                <expand macro="sanitize_query" />
            </param>

8:c1d53e95327f

#end if

## date options
#if str($time_tree.date_source.select_source) == 'dataset':
    #if $time_tree.date_source.date:
        --date '$time_tree.date_source.date'
    #end if
#elif str($time_tree.date_source.select_source) == 'input':
    --date TAXNAME
    #if str($time_tree.date_source.date_tip) != '':
        --date-tip '$time_tree.date_source.date_tip'

#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."/>
            <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output">
                <expand macro="sanitize_query" />
            </param>

            <param type="boolean" name="short_alignments" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." />

                    <option value="input">Derive from input</option>
                </param>
                <when value="none" />
                <when value="input" />
                <when value="dataset">
                    <param argument="--date" type="data" format="txt,tabular" optional="true" label="File containing dates of tips or ancestral nodes" />
                </when>
            </conditional>
            <param argument="--date-tip" type="text" optional="true" label="Tip dates as a real number or YYYY-MM-DD">
                <expand macro="sanitize_query" />
            </param>