annotate remove_chimera_macros.xml @ 0:cd7675c5b15a draft

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

<?xml version="1.0"?>
<macros>
    <token name="@REMOVE_CHIMERA_CMD_LINE@">
        remove_chimera.py
            @CPUS@
            --input-fasta '$input_fasta' 
            --input-biom '$input_biom'
            #if $long_read == "yes"
            --long-reads
            #end if
            
            --output-biom '$output_biom'
            --output-fasta '$output_fasta'
            --html '$html'

    </token>

    <xml name="remove_chimera_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." />
        <!-- Parameter -->
        <param argument="--long-read" type="select" display="radio" label="The data originally comes from long-read sequencing" help="For long reads sequencing, chimera will be detected using chimeras_denovo algorithm of vsearch (instead of uchime_denovo for short reads sequencing).">
            <option value="yes" >Yes</option>
            <option value="no" selected="true" >No</option>
		</param>
    </xml>

    <!-- Test -->
    <xml name="remove_chimera_test_input">
        <param name="input_fasta" value="references/01-reads_processing-swarm-vsearch.fasta" />
        <param name="input_biom" value="references/01-reads_processing-swarm-vsearch.biom" />
    </xml>

    <xml name="remove_chimera_test_output">
        <output name="output_fasta" file="references/03-chimera.fasta" compare="diff" lines_diff="0" />
        <output name="output_biom" file="references/03-chimera.biom" compare="sim_size" delta="0" />
        <output name="html" file="references/03-chimera.html" compare="diff" lines_diff="0" />
    </xml>
</macros>