comparison macros.xml @ 26:5f2ca10db92a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

25:f04a1264e2a2

            <option value="Blepharisma-Nuclear">Blepharisma Nuclear
            code</option>
        </param>
    </xml>

    <xml name="branches">
        <param name="branches" type="select" label="Set of branches to test">
            <option value="All">All branches</option>
            <option value="Internal">Internal branches</option>
            <option value="Leaves">Leaf branches</option>
            <option value="'Unlabeled-branches'">Unlabeled branches</option>
        </param>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/molbev/msz197</citation>
            <yield/>

        <requirements>
            <requirement type="package" version="@VERSION@">hyphy</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
    <token name="@CATCH_ERROR@"><![CDATA[
        EC=\$? ;
        if [ \$EC -ne 0 ] ; then
            if [ -f errors.log.mpinode0 ] ; then
                cat errors.log.mpinode0 >&2 ;
            else 
                cat errors.log >&2 ;
            fi ;
        fi ;
        exit \$EC
    ]]></token>
    <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
        export HYPHY=`which hyphy` &&
        export HYPHY_PATH=`dirname \$HYPHY` &&
        export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
    <token name="@HYPHY_INVOCATION@"><![CDATA[
        @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
    ]]></token>
    <token name="@SYMLINK_FILES@"><![CDATA[
        ln -s '$input_file' input.$input_file.extension &&
        ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json &&
        #set $input_file = 'input.%s' % $input_file.extension
        #if $input_nhx:
            ln -s '$input_nhx' input.nhx &&
        #end if
    ]]></token>
</macros>

26:5f2ca10db92a

            <option value="Blepharisma-Nuclear">Blepharisma Nuclear
            code</option>
        </param>
    </xml>

    <xml name="srv">
        <conditional name="advanced" label="Advanced options">
            <param name="srv_options" type="select" label="Set advanced parameters" help="If these parameters are not set, RELAX will calculate appropriate values at runtime">
                <option value="defaults">Calculate</option>
                <option value="specify">Specify values</option>
            </param>
            <when value="defaults" />
            <when value="specify">
                <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" />
                <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" />
                <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Alpha rate classes to include in the model" />
                <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" />
                <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" />
                <param name="save_alternative_model" type="boolean" label="Save alternative model fit" />
            </when>
        </conditional>
    </xml>

    <xml name="branches">
        <conditional name="branch_cond">
            <param name="branch_sel" type="select" label="Set of branches to test">
                <option value="All">All branches</option>
                <option value="Internal">Internal branches</option>
                <option value="Leaves">Leaf branches</option>
                <option value="'Unlabeled-branches'">Unlabeled branches</option>
                <option value="specify">Enter a branch label</option>
            </param>
            <when value="specify">
                <param name="branch_label" type="text" value="Test" optional="false" label="Branch label">
                    <sanitizer invalid_char="">
                        <valid initial="default" />
                    </sanitizer>
                </param>
            </when>
            <when value="All" />
            <when value="Internal" />
            <when value="Leaves" />
            <when value="'Unlabeled-branches'" />
        </conditional>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/molbev/msz197</citation>
            <yield/>

        <requirements>
            <requirement type="package" version="@VERSION@">hyphy</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="alternative_model_output">
        <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
            <filter>advanced['save_alternative_model']</filter>
        </data>
    </xml>
    <token name="@INPUT_TREE@"><![CDATA[
            #if $input_nhx:
                --tree input.nhx
            #end if
        ]]>
    </token>
    <token name="@branch_options@"><![CDATA[
        #if $branch_cond.branch_sel == 'specify':
            --branches '$branch_cond.branch_label'
        #else:
            --branches $branch_cond.branch_sel
        #end if
        ]]>
    </token>
    <token name="@advanced_options@"><![CDATA[
        #if $advanced.srv_options == 'specify':
            --grid-size $advanced.grid_size
            --starting-points $advanced.starting_points
            --syn-rates $advanced.syn_rates
            --rates $advanced.rates
            --srv $advanced.srv
            #if $advanced.save_alternative_model:
                --save-fit alternative_model.json
            #end if
        #end if
    ]]></token>
    <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
    <token name="@ERRORS@"><![CDATA[
        ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
    ]]></token>
    <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
        export HYPHY=`which hyphy` &&
        export HYPHY_PATH=`dirname \$HYPHY` &&
        export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
    <token name="@HYPHY_INVOCATION@"><![CDATA[
        @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
    ]]></token>
    <token name="@SYMLINK_FILES@"><![CDATA[
        #if $input_nhx is not None:
            ln -s '$input_nhx' input.nhx &&
        #end if
        ln -s '$input_file' input.$input_file.extension &&
        #set $input_file = 'input.%s' % $input_file.extension
    ]]></token>
</macros>