comparison phylogenomics_analysis.xml @ 56:ae197e9e9497 draft

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55:150087c2f41d

                    #if str($tree_inference_method) == 'raxml':
                        #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
                        #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
                        #if str($rooting_order_file) == 'yes':
                            --rooting_order '$rooting_order_file_cond.rooting_order'
                        #end if
                        --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
                    #end if
                    --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
                    --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size

                                <option value="raxml" selected="true">RAxML</option>
                                <option value="fasttree">FastTree</option>
                            </param>
                            <when value="raxml">
                                <conditional name="rooting_order_file_cond">
                                    <param name="rooting_order_file" type="select" label="Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?">
                                        <option value="no" selected="true">No</option>
                                        <option value="yes">Yes</option>
                                    </param>
                                    <when value="no" />
                                    <when value="yes">
                                        <param name="rooting_order" format="txt" type="data" label="History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees" />
                                    </when>
                                </conditional>
                                <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
                            </when>
                            <when value="fasttree" />

        - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.

        * **Phylogenetic trees options**

        - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
        - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
        - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** - History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
        - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
        - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
        - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.

        * **MSA quality control options**

56:ae197e9e9497

                    #if str($tree_inference_method) == 'raxml':
                        #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
                        #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
                        #if str($rooting_order_file) == 'yes':
                            --rooting_order '$rooting_order_file_cond.rooting_order'
                        #else:
                            #set default_rooting_order = $__tool_directory__/rooting_order.config
                            --rooting_order '$default_rooting_order'
                        #end if
                        --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
                    #end if
                    --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
                    --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size

                                <option value="raxml" selected="true">RAxML</option>
                                <option value="fasttree">FastTree</option>
                            </param>
                            <when value="raxml">
                                <conditional name="rooting_order_file_cond">
                                    <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select no for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
                                        <option value="no" selected="true">No</option>
                                        <option value="yes">Yes</option>
                                    </param>
                                    <when value="no" />
                                    <when value="yes">
                                        <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
                                    </when>
                                </conditional>
                                <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
                            </when>
                            <when value="fasttree" />

        - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.

        * **Phylogenetic trees options**

        - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
        - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
        - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
        - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
        - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.

        * **MSA quality control options**