annotate itsx_macros.xml @ 0:cd7675c5b15a draft

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

<?xml version="1.0"?>
<macros>
    <token name="@ITSX_CMD_LINE@">
        itsx.py
            @CPUS@
            --input-fasta '$input_fasta'
            --input-biom '$input_biom'
            --organism-groups '$organism_groups'
            
            #if $trim_sequence.check_its_only == "yes"
                --check-its-only
            #else
                --region $trim_sequence.region
            #end if

            --output-fasta '$output_fasta'
            --output-biom '$output_biom'
            --output-removed-sequences '$output_removed_sequences'
            --html '$html'
    </token>

    <xml name="itsx_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="trim_sequence">
			<param argument="--check-its-only" type="select" label="Trim conserved sequence (SSU, 5.8S, LSU) ?" help="If Yes, only part of the sequences with ITS signature will be kept. SSU, LSU or 5.8S regions will be trimmed (default : No)" display="radio">
            	<option value="yes" selected="true">No, keep conserved regions</option>
            	<option value="no" >Yes, trim conserved regions</option>
			</param>
            <when value="yes"/>
            <when value="no">
                <param argument="--region" type="select" label="ITS region" help="Which fungal ITS region is targeted: either ITS1 or ITS2 ?" display="radio">
                    <option value="ITS1">ITS1</option>
                    <option value="ITS2">ITS2</option>
                </param>
            </when>
		</conditional>
         
        <param argument="--organism-groups" type="select" multiple="true" display="checkboxes" label="Choose pertinent organisms to scan:" help="Save a lot of time by checking pertinent organism group model to scan">
            <option value="F" selected="true">Fungi</option>
            <option value="A">Alveolata</option>
            <option value="B">Bryophyta</option>
            <option value="C">Bacillariophyta</option>
            <option value="D">Amoebozoa</option>
            <option value="E">Euglenozoa</option>
            <option value="G">Chlorophyta</option>
            <option value="H">Rhodophyta</option>
            <option value="I">Phaeophyceae</option>
            <option value="L">Marchantiophyta</option>
            <option value="M">Metazoa</option>
            <option value="O">Oomycota</option>
            <option value="P">Haptophyceae</option>
            <option value="Q">Raphidophyceae</option>
            <option value="R">Rhizaria</option>
            <option value="S">Synurophyceae</option>
            <option value="T">Tracheophyta</option>
            <option value="U">Eustigmatophyceae</option>
            <!-- hmm not available in ITSx_db folder -->
            <!-- <option value="X">Apusozoa</option>
			<option value="Y">Parabasalia</option> -->
        </param>
    </xml>

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

        <!-- Parameters -->
        <conditional name="trim_sequence">
			<param name="check_its_only" value="no" />
            <param name="region" value="ITS1" />
        </conditional>
    </xml>

    <xml name="itsx_test_output">
        <output name="output_biom" file="references/05-itsx.biom" compare="diff" lines_diff="0" />
        <output name="output_fasta" file="references/05-itsx.fasta" compare="sim_size" delta="0" /> <!--same content but could be in a different order -->
        <output name="output_removed_sequences" file="references/05-itsx-excluded.fasta" compare="diff" lines_diff="0" />
        <output name="html" file="references/05-itsx.html" compare="diff" lines_diff="0" />
    </xml>
</macros>