comparison macros.xml @ 45:e668628f62b7 draft

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44:58382c8ed01c

    <xml name="requirements_kaks_analysis">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
        </requirements>
    </xml>
    <xml name="requirements_gene_family_phylogeny_builder">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
        </requirements>
    </xml>

            <regex match="Error:"/>
            <regex match="Exception:"/>
        </stdio>
    </xml>
    <xml name="param_codon_alignments">
        <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments">
            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
        </param>
    </xml>
    <xml name="param_method">

                <option value="mafft" selected="true">MAFFT</option>
                <option value="pasta">PASTA</option>
            </param>
            <when value="mafft" />
            <when value="pasta">
                <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
            </when>
        </conditional>
    </xml>
    <xml name="cond_remove_gappy_sequences">
        <conditional name="remove_gappy_sequences_cond">

45:e668628f62b7

    <xml name="requirements_kaks_analysis">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
        </requirements>
    </xml>
    <xml name="requirements_ks_distribution">
        <requirements>
            <requirement type="package" version="1.3.0">r-optparse</requirement>
        </requirements>
    </xml>
    <xml name="requirements_gene_family_phylogeny_builder">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
        </requirements>
    </xml>

            <regex match="Error:"/>
            <regex match="Exception:"/>
        </stdio>
    </xml>
    <xml name="param_codon_alignments">
        <param name="codon_alignments" type="select" label="Codon alignments">
            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
        </param>
    </xml>
    <xml name="param_method">

                <option value="mafft" selected="true">MAFFT</option>
                <option value="pasta">PASTA</option>
            </param>
            <when value="mafft" />
            <when value="pasta">
                <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
            </when>
        </conditional>
    </xml>
    <xml name="cond_remove_gappy_sequences">
        <conditional name="remove_gappy_sequences_cond">