annotate affiliation_postprocess_macros.xml @ 2:76ff9af5c0a3 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e987ae3594883fb3b12d2999c6ad7fccd0b1b64

<?xml version="1.0"?>
<macros>
    <token name="@AFFILIATION_POSTPROCESS_CMD_LINE@">
        affiliation_postprocess.py
            --input-biom '$input_biom'
            --input-fasta '$input_fasta'

            #if $is_HVL.HVL_amplicon == "Yes"
                --reference '$is_HVL.reference.fields.path'
            #end if
            
            --identity $identity
            --coverage $coverage

            --output-biom '$output_biom'
            --output-fasta '$output_fasta'
            --output-compo '$output_asv_compo'
    </token>

    <xml name="affiliation_postprocess_inputs">
        <!-- Files -->
        <param argument="--input-fasta" type="data" format="fasta" label="Sequence file (.fasta)" help="The sequence file to filter." />
        <param argument="--input-biom" type="data" format="biom1" label="Abundance file (.biom)" help="The abundance file to filter." />

        <!-- Parameters -->
        <conditional name="is_HVL">
            <param name="HVL_amplicon" type="select" display="radio" label="Is this an amplicon hyper variable in length?" help="Multi-affiliation tag may be resolved by selecting the shortest amplicon reference. For this, you need the reference fasta file of your target amplicon.">
                <option value="No">No</option>
                <option value="Yes" >Yes</option>
            </param>
            <when value="Yes">
                <param argument="--reference" type="select" label="Using reference database" help="Select reference from the list">
                    <options from_data_table="frogs_HVL_db"/>
                    <validator type="no_options" message="A built-in database is not available"/>
                </param>
            </when>
            <when value="No"/>
        </conditional>
        <param argument="--identity" type="float" min="0.0" max="100.0" value="99.0" label="Minimum identity for aggregation" help="ASVs will be aggregated if they share the same taxonomy with at least X% identity"/>
        <param argument="--coverage" type="float" min="0.0" max="100.0" value="99.0" label="Minimum coverage for aggregation" help="ASVs will be aggregated if they share the same taxonomy with at least X% alignment coverage"/>
    </xml>

    <!-- Test -->
    <xml name="affiliation_postprocess_test_input">
        <param name="input_fasta" value="references/04-filters.fasta" />
        <param name="input_biom" value="references/06-affiliation.biom" />

        <conditional name="is_HVL">
            <param name="HVL_amplicon" value="Yes" />
            <param name="reference" value="Unite_extract_ITS1_test" />
        </conditional>
    </xml>
    
    <xml name="affiliation_postprocess_test_output">
        <!-- Diff size instead of line because biom include date -->
        <output name="output_biom" file="references/08-affiliation_postprocessed.biom" compare="sim_size" delta="0"  />
        <output name="output_fasta" file="references/08-affiliation_postprocessed.fasta" compare="diff" lines_diff="0" />
        <output name="output_asv_compo" file="references/08-affiliation_postprocessed.compo.tsv" compare="diff" lines_diff="0" />
    </xml>  
</macros>