comparison iqtree.xml @ 7:524d31add34a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"

6:224c75ad0518

## file
#if $general_options.s
    -s '$general_options.s'
#end if

## file
#if $general_options.t
    -t '$general_options.t'
    $tree_parameters.constructing_consensus.con_tree
    $tree_parameters.constructing_consensus.con_net

]]>
    </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 type="boolean" name="short_alignments" truevalue="true" falsevalue="false" 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." />
            <param argument="--seqtype" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences">
                <help><![CDATA[
Note that --seqtype CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code.
<br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like --seqtype NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
                </help>

        <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
        <data name="contree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
        <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
        <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
        <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
        <data name="mlrate" format="data" from_work_dir="*.mlrate" label="">
            <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="6">
            <param name="seed" value="1257" />

            <param name="s" value="short.fasta" />
            <param name="short_alignments" value="true" />
            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

7:524d31add34a

## file
#if $general_options.s
    -s '$general_options.s'
#end if

#if $general_options.o
    -o '$general_options.o'
#end if

## file
#if $general_options.t
    -t '$general_options.t'
    $tree_parameters.constructing_consensus.con_tree
    $tree_parameters.constructing_consensus.con_net

]]>
    </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." />
            <param argument="--seqtype" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences">
                <help><![CDATA[
Note that --seqtype CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code.
<br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like --seqtype NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
                </help>

        <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
        <data name="contree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
        <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
        <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
        <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
        <data name="mlrate" format="data" from_work_dir="*.mlrate" label="${tool.name} on ${on_string}: ML Rates">
            <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
        </data>
        <data name="timetree" format="nex" from_work_dir="PREF.timetree.nex" label="${tool.name} on ${on_string}: Tree labeled with dates">
            <filter>time_tree['date_source']['select_source'] != 'none'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="6">
            <param name="seed" value="1257" />

            <param name="s" value="short.fasta" />
            <param name="short_alignments" value="true" />
            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="7">
            <param name="s" value="dates.fa" />
            <param name="n" value="100" />
            <param name="seed" value="122125" />
            <param name="select_source" value="dataset" />
            <param name="date" value="dates.tabular" />
            <output name="timetree">
                <assert_contents>
                    <has_line_matching expression=".+222-3pu_03-28-01_985737600.+" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[