comparison macros.xml @ 91:79573009efe0 draft

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90:6c1cfd0be856

            <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
            <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
            <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
        </param>
    </xml>
    <xml name="whens_multiple_sequence_alignments_option_cond">
        <when value="create_alignments" />
        <when value="add_alignments" />
        <when value="pasta_alignments">
            <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />

            <when value="no" />
            <when value="yes">
                <conditional name="multiple_sequence_alignments_option_cond">
                    <expand macro="whens_multiple_sequence_alignments_option_cond" />
                    <expand macro="param_multiple_sequence_alignments_option" />
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="cond_phylogenetic_trees_ptortho">

                <conditional name="remove_sequences_with_gaps_cond">
                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
                        <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
                        <expand macro="cond_multiple_sequence_alignments" />
                    </when>
                </conditional>
                <expand macro="cond_multiple_sequence_alignments" />
            </when>
        </conditional>
    </xml>
    <xml name="param_multiple_codon_alignments">
        <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">

91:79573009efe0

            <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
            <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
            <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
        </param>
    </xml>
    <xml name="cond_multiple_sequence_alignments_option_with_iterative_realignments">
        <conditional name="multiple_sequence_alignments_option_cond">
            <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
                <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
                <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
                <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
                <option value="iterative_realignments">Iterative orthogroups realignment, trimming and fitering</option>
            </param>
            <expand macro="whens_multiple_sequence_alignments_option_cond" />
            <when value="iterative_realignments">
                <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
            </when>
        </conditional>
    </xml>
    <xml name="whens_multiple_sequence_alignments_option_cond">
        <when value="create_alignments" />
        <when value="add_alignments" />
        <when value="pasta_alignments">
            <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />

            <when value="no" />
            <when value="yes">
                <conditional name="multiple_sequence_alignments_option_cond">
                    <expand macro="whens_multiple_sequence_alignments_option_cond" />
                    <expand macro="param_multiple_sequence_alignments_option" />
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="cond_multiple_sequence_alignments_with_iterative_realignments">
        <conditional name="multiple_sequence_alignments_cond">
            <expand macro="param_multiple_sequence_alignments" />
            <when value="no" />
            <when value="yes">
                <conditional name="multiple_sequence_alignments_option_cond">
                    <expand macro="whens_multiple_sequence_alignments_option_cond" />
                    <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignments" />
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="cond_phylogenetic_trees_ptortho">

                <conditional name="remove_sequences_with_gaps_cond">
                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no">
                        <expand macro="cond_multiple_sequence_alignments" />
                    </when>
                    <when value="yes">
                        <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
                        <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
                        <expand macro="cond_multiple_sequence_alignments_with_iterative_realignments" />
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="param_multiple_codon_alignments">
        <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">