comparison sina.xml @ 2:49b937f12aa4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina commit e94aa6daf5746ddd3798b8b3d8bc92094b03be90"

1:fd62f1b940f6

<tool id="sina" name="SINA" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
    <description>reference based multiple sequence alignment</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ## initialize
        ## parse custom reference from fasta to arb file format

        #if $db.select == 'custom'
            #if $db.custom.ext == 'fasta'
                sina -i '$db.custom' --prealigned -o ./reference.arb &&
            #else
                ln -s '$db.custom' ./reference.arb && 
            #end if
        #elif $db.select == 'local'
            ln -s '$db.arb_databases.fields.path' ./reference.arb &&
        #end if

        ## run
        sina
            --in='$in'
            --db=./reference.arb
            -p \${GALAXY_SLOTS:-4}
            --num-pts=\${GALAXY_SLOTS:-4}

            #if $os.type == 'arb'
                --outtype='arb'

        </test>
        <!-- #6 in: *.fasta; db: <arb_databases>.arb; out: *.fasta; standard parameters -->
        <test>
            <param name="in" value="sequence.fasta"/>
            <conditional name="db">
                <param name="select" value="local"/> 
                <param name="arb_databases" value="testarb"/>
            </conditional>
            <section name="os">
                <param name="type" value="arb"/>
            </section>

2:49b937f12aa4

<tool id="sina" name="SINA" version="@TOOL_VERSION@+@WRAPPER_VERSION@" profile="18.01">
    <description>reference based multiple sequence alignment</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ## initialize
        ## parse custom reference from fasta to arb file format

        #if $db.select == 'custom'
            #if $db.custom.ext == 'fasta'
                sina -i '$db.custom' --prealigned -o reference.arb &&
            #else
                ln -s '$db.custom' reference.arb &&
            #end if
        #elif $db.select == 'local'
            ln -s '$db.arb_databases.fields.path' reference.arb &&
        #end if

        ## run
        sina
            --in='$in'
            --db=reference.arb
            -p \${GALAXY_SLOTS:-4}
            --num-pts=\${GALAXY_SLOTS:-4}

            #if $os.type == 'arb'
                --outtype='arb'

        </test>
        <!-- #6 in: *.fasta; db: <arb_databases>.arb; out: *.fasta; standard parameters -->
        <test>
            <param name="in" value="sequence.fasta"/>
            <conditional name="db">
                <param name="select" value="local"/>
                <param name="arb_databases" value="testarb"/>
            </conditional>
            <section name="os">
                <param name="type" value="arb"/>
            </section>