annotate picrust2_pathways_macros.xml @ 0:c5fd7b97c2a4 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a

<?xml version="1.0"?>
<macros>
    <token name="@PICRUST2_PATHWAYS_CMD_LINE@">
        frogsfunc_pathways.py
            @CPUS@
            --input-tsv '$input_tsv'
            --map $database.fields.path

          #if $normalisation
            --normalisation
          #end if

          --html $html
          --output-pathways-abund '$output_pathways_abund'
    </token>

    <xml name="picrust2_pathways_inputs">
        <!-- Files -->
        <param argument="--input-tsv" format="tsv" type="data" label="Function abundance file (format Tsv)" help="Function TSV abundance (output of picrust2_functions tool : EC_unstrat_abundance.tsv or KO_unstrat_abundance.tsv)." optional="false"/>

        <!-- References -->
        <param name="marker" type="select" multiple="false" display="radio" label="Marker gene" help="Marker gene analysed.">
            <options from_data_table="frogs_picrust2_pathways">
                <column name='name' index='2' />
                <column name='value' index='2' />
                <filter type="unique_value" column='2'/>
                    <validator type="no_options" message="A built-in database is not available" />
            </options>
        </param>
        <param name="database" type='select' label="Pathway reference database" help="For 16S marker, choose Metacyc (EC functions) or KEGG (KO functions) in accordance with your function abundance input file. For fungi ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'>
            <options from_data_table="frogs_picrust2_pathways">
                <column name='name' index='1'/>
                <column name='value' index='1'/>
                <column name='path' index='3'/>
                <filter type="param_value" ref="marker" column="2" />               
                <validator type="no_options" message="A built-in database is not available" />
            </options>
        </param>

        <!-- Parameters-->
        <param argument="--normalisation" label="Do you want to normalize the final output table ?" help='Values are divided by sum of columns, then multiplied by 10^6 (CPM values).' type="boolean" />
    </xml>

    <!-- Test -->
    <xml name="picrust2_pathways_test_input">
        <param name="input_tsv" value="references/26-frogsfunc_functions_unstrat_EC.tsv" />
        <param name="marker" value="16S" />
        <param name="database" value="Metacyc" />
    </xml>

    <xml name="picrust2_pathways_test_output">
        <output name="output_pathways_abund" file="references/27-frogsfunc_pathways_unstrat.tsv" compare="diff" lines_diff="0" />
        <output name="html" file="references/27-frogsfunc_pathways_summary.html" compare="diff" lines_diff="0" />
    </xml>       
</macros>