comparison macros.xml @ 24:ec499ddce7a9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

23:599e492f8063

<?xml version="1.0"?>
<macros>
    <xml name="inputs">
        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
        <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
    </xml>
    <xml name="substitution">
        <param name="model" type="select" label="Substitution model">
            <option value="GTR">GTR - General time reversible
            model</option>

        <citations>
            <citation type="doi">10.1093/molbev/msz197</citation>
            <yield/>
        </citations>
    </xml>
    <token name="@VERSION@">2.5.30</token>
    <xml name="requirements">
        <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_MPIERR@"><![CDATA[
        EC=\$? ;
        if [ \$EC -ne 0 ] ; then
            cat errors.log.mpinode0 >&2 ;
        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>
</macros>

24:ec499ddce7a9

<?xml version="1.0"?>
<macros>
    <xml name="inputs">
	    <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
        <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
    </xml>
    <xml name="substitution">
        <param name="model" type="select" label="Substitution model">
            <option value="GTR">GTR - General time reversible
            model</option>

        <citations>
            <citation type="doi">10.1093/molbev/msz197</citation>
            <yield/>
        </citations>
    </xml>
    <token name="@VERSION@">2.5.31</token>
    <xml name="requirements">
        <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>