annotate affiliation_report_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_REPORT_CMD_LINE@">
        affiliation_report.py
            --input-biom '$input_biom'

            --taxonomic-ranks $taxonomic_ranks
            --rarefaction-ranks $rarefaction_ranks

            #if $affiliation.affiliation_type == "FROGS_blast"
                --multiple-tag 'blast_affiliations'
                --tax-consensus-tag 'blast_taxonomy'
                --identity-tag 'perc_identity'
                --coverage-tag 'perc_query_coverage'
            #elif $affiliation.affiliation_type == "FROGS_rdp"
                --taxonomy-tag 'rdp_taxonomy'
                --bootstrap-tag 'rdp_bootstrap'
            #else
                --taxonomy-tag '$affiliation.taxonomy_tag'

                #if $affiliation.bootstrap_tag
                    --bootstrap-tag '$affiliation.bootstrap_tag'
                #end if

                #if $affiliation.identity_tag and $affiliation.coverage_tag
                    --identity-tag '$affiliation.identity_tag'
                    --coverage-tag '$affiliation.coverage_tag'
                #end if
                
            #end if

            --html '$html'
    </token>

    <xml name="affiliation_report_inputs">
        <!-- Files -->
        <param argument="--input-biom" type="data" format="biom1" label="Abundance file (format: BIOM)" help="The abundance file to filter." />
        <!-- Parameters -->
		<expand macro="taxonomic_ranks"/>
		<param argument="--rarefaction-ranks" type="text" optional="false" value="Class Order Family Genus Species" 
			label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space.">
			<expand macro="only_letter_sanitizer_validator"/>
		</param>
		<conditional name="affiliation">
			<param name="affiliation_type" type="select" label="Affiliation to process" help="Select the type of affiliation to process. If your affiliation was generated with an external tool: use 'Custom'.">
				<option value="FROGS_blast" selected="true">FROGS Blast</option>
				<option value="FROGS_rdp">FROGS RDP</option>
				<option value="custom">Custom</option>
			</param>
			<when value="FROGS_blast"/>
			<when value="FROGS_rdp"/>
			<when value="custom">
				<param argument="--taxonomy-tag" type="text" value="taxonomy" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy">
					<expand macro="restricted_sanitizer_validator"/>
				</param>
				<param argument="--bootstrap-tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap">
					<expand macro="restricted_sanitizer_validator"/>
				</param>
				<param argument="--identity-tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity">
					<expand macro="restricted_sanitizer_validator"/>
				</param>
				<param argument="--coverage-tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment ASVs coverage">
					<expand macro="restricted_sanitizer_validator"/>
				</param>
			</when>
		</conditional>
    </xml>

    <!-- Test -->
    <xml name="affiliation_report_test_input">
        <param name="input_biom" value="references/09-normalisation.biom" />
        <param name="rarefaction_ranks" value="Family Genus Species" />
    </xml>
    
    <xml name="affiliation_report_test_output">
        <output name="html" file="references/11-affiliation_report.html" compare="diff" lines_diff="2" />
    </xml>     
</macros>