annotate tree_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="@TREE_CMD_LINE@">
        tree.py
            --input-fasta '$input_fasta'
            --input-biom '$input_biom'
            @CPUS@
            --output-tree '$output_tree'
            --html '$html'
    </token>

    <xml name="tree_inputs">
        <!-- Files -->
        <param argument="--input-fasta" type="data" format="fasta" label="Sequence file (.fasta)" help="FASTA file containing the representative sequences to be used for phylogenetic tree construction." />
        <param argument="--input-biom" type="data" format="biom1" label="Abundance file (.biom)" help="BIOM file containing the abundance table associated with the input sequences." />
    </xml>

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

    <xml name="tree_test_output">
        <output name="output_tree" file="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
        <output name="html" file="references/15-tree-mafft.html" compare="diff" lines_diff="2" />
        <output name="html">
            <assert_contents>
                <has_text_matching expression="FROGS\sTree" />
                <has_text_matching expression="abundance_removed.*:\s0" />
                <has_text_matching expression="abundance_kept.*:\s73531" />
                <has_text_matching expression="asv_removed.*:\s0" />
                <has_text_matching expression="asv_kept.*:\s54" />
            </assert_contents>
        </output>
    </xml>
</macros>