comparison iqtree.xml @ 4:f97743d52b87 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"

3:973a28be3b7f

    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors='exit_code' ><![CDATA[
iqtree
    -pre PREF
    -nt \${GALAXY_SLOTS:-10}
    -redo

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

$bootstrap_parameters.nonparametric_bootstrap.bo

#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" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
            <param argument="-st" 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 -st 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 -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
                </help>

                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 ${on_string}: MaxLikelihood Tree" />
        <data name='contree' format='nhx' from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
        <data name='mldist' format='mldist' from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
        <data name='splits.nex' format='nex' from_work_dir="*.splits.nex" label="${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" />
    </outputs>
    <tests>
        <test>
            <param name="seed" value="1257" />
            <param name="st" value="AA" />

            <param name="m" value="TESTNEW" />
            <param name="msub" value="nuclear" />
            <param name="madd" value="LG4M,LG4X" />
            <param name="merit" value="AICc" />
            <param name="bb" value="1000" />
            <output name='bionj'>
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>
            </output>
            <output name='iqtree'>
                <assert_contents>
                    <has_text_matching expression="VT\+F\+R3(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>
            <output name='mldist'>
                <assert_contents>
                    <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" />
                    <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
                    <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
                </assert_contents>
            </output>
            <output name='treefile'>
                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
            <output name='contree' >
                <assert_contents>
                    <has_line_matching
                        expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
                </assert_contents>
            </output>
            <output name='splits.nex'>
                <assert_contents>
                    <has_line line="BEGIN Splits;" />
                    <has_line line="END; [Splits]" />
                </assert_contents>
            </output>

            <param name="nm" value="1000" />
            <param name="bcor" value="0.99" />
            <param name="nstep" value="100" />
            <param name="beps" value="0.5" />
            <param name="b" value="2" />
            <output name='iqtree'>
                <assert_contents>
                    <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>
            <output name='treefile'>
                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>

            <param name="nm" value="1000" />
            <param name="bcor" value="0.99" />
            <param name="nstep" value="100" />
            <param name="beps" value="0.5" />
            <!-- <param name="b" value="100" /> -->
            <output name='iqtree'>
                <assert_contents>
                    <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>
            <output name='treefile'>
                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name='s' value='example.phy' />
            <output name='iqtree'>
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>
            </output>
            <output name='treefile'>
                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name='s' value='example.phy' />
            <param name='opt_custommodel' value='true' />
            <param name='m' value='GTR+G{0.9}' />
            <output name='iqtree'>
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>
            </output>
            <output name='treefile'>
                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
IQ-TREE
=======

4:f97743d52b87

    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
iqtree
    -pre PREF
    #if $general_options.short_alignments:
        -nt 1
    #else:
        -nt \${GALAXY_SLOTS:-10}
    #end if
    -redo

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

$bootstrap_parameters.nonparametric_bootstrap.bo

#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" 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="-st" 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 -st 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 -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
                </help>

                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 ${on_string}: MaxLikelihood Tree" />
        <data name="contree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
        <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
        <data name="splits.nex" format="nex" from_work_dir="*.splits.nex" label="${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" />
    </outputs>
    <tests>
        <test>
            <param name="seed" value="1257" />
            <param name="st" value="AA" />

            <param name="m" value="TESTNEW" />
            <param name="msub" value="nuclear" />
            <param name="madd" value="LG4M,LG4X" />
            <param name="merit" value="AICc" />
            <param name="bb" value="1000" />
            <output name="bionj">
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>
            </output>
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression="VT\+F\+R3(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>
            <output name="mldist">
                <assert_contents>
                    <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" />
                    <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
                    <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
                </assert_contents>
            </output>
            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
            <output name="contree">
                <assert_contents>
                    <has_line_matching
                        expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
                </assert_contents>
            </output>
            <output name="splits.nex">
                <assert_contents>
                    <has_line line="BEGIN Splits;" />
                    <has_line line="END; [Splits]" />
                </assert_contents>
            </output>

            <param name="nm" value="1000" />
            <param name="bcor" value="0.99" />
            <param name="nstep" value="100" />
            <param name="beps" value="0.5" />
            <param name="b" value="2" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>
            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>

            <param name="nm" value="1000" />
            <param name="bcor" value="0.99" />
            <param name="nstep" value="100" />
            <param name="beps" value="0.5" />
            <!-- <param name="b" value="100" /> -->
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>
            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="s" value="example.phy" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>
            </output>
            <output name="treefile">
                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="s" value="example.phy" />
            <param name="opt_custommodel" value="true" />
            <param name="m" value="GTR+G{0.9}" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>
            </output>
            <output name="treefile">
                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="s" value="short.fasta" />
            <param name="short_alignments" value="true" />
        </test>
    </tests>
    <help><![CDATA[
IQ-TREE
=======