comparison macros.xml @ 88:5f64fcf4437a draft

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87:6154253af263

            <when value="yes">
                <conditional name="options_type_cond">
                    <expand macro="param_options_type" />
                    <when value="basic" />
                    <when value="advanced">
                        <expand macro="cond_multiple_sequence_alignments" />
                        <expand macro="cond_phylogenetic_trees_ptorthocs" />
                        <expand macro="cond_remove_gappy_sequences" />
                        <expand macro="param_multiple_codon_alignments" />
                    </when>
                </conditional>
            </when>
            <when value="no">
                <conditional name="options_type_cond">
                    <expand macro="param_options_type" />
                    <when value="basic" />
                    <when value="advanced">
                        <expand macro="cond_multiple_sequence_alignments" />
                        <expand macro="cond_phylogenetic_trees_ptorthocs" />
                        <expand macro="cond_remove_gappy_sequences" />
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>

        <conditional name="remove_gappy_sequences_cond">
            <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <conditional name="trim_type_cond">
                    <param name="trim_type" type="select" label="Select process used for gap trimming">
                        <option value="gap_trimming" selected="true">Nucleotide based </option>
                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</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"/>
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>

88:5f64fcf4437a

            <when value="yes">
                <conditional name="options_type_cond">
                    <expand macro="param_options_type" />
                    <when value="basic" />
                    <when value="advanced">
                        <expand macro="cond_remove_gappy_sequences" />
                        <expand macro="cond_phylogenetic_trees_ptorthocs" />
                        <expand macro="param_multiple_codon_alignments" />
                    </when>
                </conditional>
            </when>
            <when value="no">
                <conditional name="options_type_cond">
                    <expand macro="param_options_type" />
                    <when value="basic" />
                    <when value="advanced">
                        <expand macro="cond_remove_gappy_sequences" />
                        <expand macro="cond_phylogenetic_trees_ptorthocs" />
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>

        <conditional name="remove_gappy_sequences_cond">
            <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
                <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">
                <conditional name="trim_type_cond">
                    <param name="trim_type" type="select" label="Select process used for gap trimming">
                        <option value="gap_trimming" selected="true">Nucleotide based </option>
                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</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>
            </when>
        </conditional>
    </xml>