comparison iqtree.xml @ 11:563c3aa769f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"

10:b8476e82ac20

<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+@VERSION_SUFFIX@" >
    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <token name="@VERSION_SUFFIX@">galaxy1</token>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
iqtree

#end if

## file
#if $general_options.t
    -t '$general_options.t'
    $tree_parameters.constructing_consensus.con_tree
    $tree_parameters.constructing_consensus.con_net
    #if str($tree_parameters.constructing_consensus.burnin) != ''
        --burnin '$tree_parameters.constructing_consensus.burnin'
    #end if

    ## file

    #if str($tree_parameters.constructing_consensus.suptag) != ''
        --suptag '$tree_parameters.constructing_consensus.suptag'
    #end if

    ## file
    #if $tree_parameters.computing_robinson_foulds.rf
        -rf '$tree_parameters.computing_robinson_foulds.rf'
        $tree_parameters.computing_robinson_foulds.tree_dist_all
        $tree_parameters.computing_robinson_foulds.rf_adj
    #end if
    $tree_parameters.ancestral_state.ancestral
    #if $tree_parameters.ancestral_state.asr_min:
        --asr-min $tree_parameters.ancestral_state.asr_min
    #end if

                <param argument="--test" type="integer" optional="true" label="Specify the number of RELL (Kishino et al., 1990) replicates (&gt;=1000) to perform several tree topology tests for all trees passed via -z" help="The tests include bootstrap proportion (BP), KH test (Kishino and Hasegawa, 1989), SH test (Shimodaira and Hasegawa, 1999) and expected likelihood weights (ELW) (Strimmer and Rambaut, 2002)."/>
                <param argument="--test-weight" type="boolean" truevalue="--test-weight" falsevalue="" checked="false" label="Used together with --test to additionally perform the weighted-KH and weighted-SH tests."/>
                <param argument="--test-au" type="boolean" truevalue="--test-au" falsevalue="" checked="false" label="Used together with --test to additionally perform the approximately unbiased (AU) test (Shimodaira, 2002)" help="Note that you have to specify the number of replicates for the AU test via -test."/>
            </section>
            <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
                <param argument="--con-tree" type="boolean" truevalue="--con-tree" falsevalue="" checked="false" label="Compute consensus tree of the trees passed via -t" help="Resulting consensus tree is written to .contree file."/>
                <param argument="--con-net" type="boolean" truevalue="--con-net" falsevalue="" checked="false" label="Compute consensus network of the trees passed via -t" help="Resulting consensus network is written to .nex file."/>
                <param argument="--sup-min" type="float" value="0.0" optional="true" label="Specify a minimum threshold (between 0 and 1) to keep branches in the consensus tree"/>
                <param argument="--burnin" type="integer" optional="true" label="Specify a burn-in, which is the number of beginning trees passed via -t to discard before consensus construction" help="This is useful e.g. when summarizing trees from MrBayes analysis."/>
                <param argument="--support" type="data" format="nhx" optional="true" label="Specify an input “target” tree file" help="That means, support values are first extracted from the trees passed via -t, and then mapped onto the target tree. Resulting tree with assigned support values is written to .suptree file. This option is useful to map and compare support values from different approaches onto a single tree."/>
                <param argument="--suptag" type="text" optional="true" label="Specify name of a node in -sup target tree" help="The corresponding node of .suptree will then be assigned with IDs of trees where this node appears. Special option --suptag ALL will assign such IDs for all nodes of the target tree."/>
            </section>

        </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 ${on_string}: MaxLikelihood Distance Matrix"/>
        <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${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 name="lsd_report" format="txt" from_work_dir="PREF.timetree.lsd" label="${tool.name} on ${on_string}: LSD Report">
            <filter>time_tree['date_source']['select_source'] != 'none'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="6">
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TEST" />
            <param name="msub" value="nuclear" />

            <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>

                    <has_line line="BEGIN Splits;" />
                    <has_line line="END; [Splits]" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <!-- bootstrap sans model -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <!-- <param name="m" value="TESTONLY" /> -->

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <!-- model sans bootstrap -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TESTONLY" />

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="s" value="example.phy" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <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>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <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="8">
            <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" />

11:563c3aa769f2

<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+@VERSION_SUFFIX@" >
    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <token name="@VERSION_SUFFIX@">galaxy2</token>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
iqtree

#end if

## file
#if $general_options.t
    -t '$general_options.t'
    $tree_parameters.constructing_consensus.contree
    $tree_parameters.constructing_consensus.connet
    #if str($tree_parameters.constructing_consensus.burnin) != ''
        --burnin '$tree_parameters.constructing_consensus.burnin'
    #end if

    ## file

    #if str($tree_parameters.constructing_consensus.suptag) != ''
        --suptag '$tree_parameters.constructing_consensus.suptag'
    #end if

    ## file
    #if $tree_parameters.computing_robinson_foulds.tree_dist_all
        $tree_parameters.computing_robinson_foulds.tree_dist_all
        --tree-dist $tree_parameters.computing_robinson_foulds.tree_dist
        --tree-dist2 $tree_parameters.computing_robinson_foulds.tree_dist2
    #end if
    $tree_parameters.ancestral_state.ancestral
    #if $tree_parameters.ancestral_state.asr_min:
        --asr-min $tree_parameters.ancestral_state.asr_min
    #end if

                <param argument="--test" type="integer" optional="true" label="Specify the number of RELL (Kishino et al., 1990) replicates (&gt;=1000) to perform several tree topology tests for all trees passed via -z" help="The tests include bootstrap proportion (BP), KH test (Kishino and Hasegawa, 1989), SH test (Shimodaira and Hasegawa, 1999) and expected likelihood weights (ELW) (Strimmer and Rambaut, 2002)."/>
                <param argument="--test-weight" type="boolean" truevalue="--test-weight" falsevalue="" checked="false" label="Used together with --test to additionally perform the weighted-KH and weighted-SH tests."/>
                <param argument="--test-au" type="boolean" truevalue="--test-au" falsevalue="" checked="false" label="Used together with --test to additionally perform the approximately unbiased (AU) test (Shimodaira, 2002)" help="Note that you have to specify the number of replicates for the AU test via -test."/>
            </section>
            <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
                <param argument="--contree" type="boolean" truevalue="--contree" falsevalue="" checked="false" label="Compute consensus tree of the trees passed via -t" help="Resulting consensus tree is written to .contree file."/>
                <param argument="--connet" type="boolean" truevalue="--connet" falsevalue="" checked="false" label="Compute consensus network of the trees passed via -t" help="Resulting consensus network is written to .nex file."/>
                <param argument="--sup-min" type="float" value="0.0" optional="true" label="Specify a minimum threshold (between 0 and 1) to keep branches in the consensus tree"/>
                <param argument="--burnin" type="integer" optional="true" label="Specify a burn-in, which is the number of beginning trees passed via -t to discard before consensus construction" help="This is useful e.g. when summarizing trees from MrBayes analysis."/>
                <param argument="--support" type="data" format="nhx" optional="true" label="Specify an input “target” tree file" help="That means, support values are first extracted from the trees passed via -t, and then mapped onto the target tree. Resulting tree with assigned support values is written to .suptree file. This option is useful to map and compare support values from different approaches onto a single tree."/>
                <param argument="--suptag" type="text" optional="true" label="Specify name of a node in -sup target tree" help="The corresponding node of .suptree will then be assigned with IDs of trees where this node appears. Special option --suptag ALL will assign such IDs for all nodes of the target tree."/>
            </section>

        </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 ${on_string}: MaxLikelihood Tree" />
        <data name="consensus_tree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree">
            <filter>tree_parameters['constructing_consensus']['contree']</filter>
        </data>
        <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${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 name="lsd_report" format="txt" from_work_dir="PREF.timetree.lsd" label="${tool.name} on ${on_string}: LSD Report">
            <filter>time_tree['date_source']['select_source'] != 'none'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TEST" />
            <param name="msub" value="nuclear" />

            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
            <output name="consensus_tree">
                <assert_contents>
                    <has_line_matching
                        expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
                </assert_contents>
            </output>

                    <has_line line="BEGIN Splits;" />
                    <has_line line="END; [Splits]" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <!-- bootstrap sans model -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <!-- <param name="m" value="TESTONLY" /> -->

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <!-- model sans bootstrap -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TESTONLY" />

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="s" value="example.phy" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <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>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <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" />