comparison macros.xml @ 4:aaeb63501369 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit ec15da3a30507841856303de991cbe80c65128fd-dirty

3:18ece3d5bcde

        <conditional name="db">
            <param name="db_src" value="cached"/>
            <param name="cat_builtin" value="CAT_prepare_test"/>
        </conditional>
    </xml>

    <xml name="use_intermediates">
        <conditional name="previous">
            <param name="use_previous" type="select" label="Use previous gene prediction and diamond alignment">
                <option value="no">No</option>
                <option value="yes">Yes</option>

    </xml>
    <token name="@CUSTOM_SETTINGS@"><![CDATA[
      --range $range
      --fraction $fraction
]]></token>
    <xml name="add_names_options">
        <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true" 
            label="Only output official level names."/>
        <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false" 
            label="Exclude bit-score support scores in the lineage."/>

4:aaeb63501369

        <conditional name="db">
            <param name="db_src" value="cached"/>
            <param name="cat_builtin" value="CAT_prepare_test"/>
        </conditional>
    </xml>
    <xml name="use_intermediates">
        <conditional name="previous">
            <param name="use_previous" type="select" label="Use previous gene prediction and diamond alignment">
                <option value="no">No</option>
                <option value="yes">Yes</option>

    </xml>
    <token name="@CUSTOM_SETTINGS@"><![CDATA[
      --range $range
      --fraction $fraction
]]></token>
    <xml name="diamond_options">
        <conditional name="diamond">
            <param name="set_diamond_opts" type="select" label="Advanced diamond options">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" 
                    label="Run DIAMOND in sensitive mode (considerably slower)"/>
                <param argument="--block_size" type="float" value="2.0" min="1" max="10" label="DIAMOND block-size parameter."
                    help="lower will decrease memory and temporary disk space usage, higher will increase performance."/>
                <param argument="--index_chunks" type="integer" value="4" min="1" max="10" label="DIAMOND index-chunks parameter" 
                    help="Set to 1 on high memory machines. The parameter has no effect on temporary disk space usage."/>
                <param argument="--top" type="integer" value="50" min="1" max="50" label="DIAMOND top parameter" 
                    help="Governs hits within range of best hit that are written to the alignment file. This implies you know what you are doing."/>
            </when>
        </conditional>
    </xml>
    <token name="@DIAMOND_OPTIONS@"><![CDATA[
        #if $diamond.set_diamond_opts == 'yes':
            $diamond.sensitive
            --block_size $diamond.block_size
            --index_chunks $diamond.index_chunks
            #if $diamond.top < 50:
                --I_know_what_Im_doing
                --top $diamond.top
            #end if
        #end if
]]></token>

    <xml name="add_names_options">
        <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true" 
            label="Only output official level names."/>
        <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false" 
            label="Exclude bit-score support scores in the lineage."/>