comparison gene_family_phylogeny_builder.xml @ 4:1134528b93cc draft

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3:d939b663bf62

    --output_phylip_dir '$output_phylip.files_path'
#end if
--min_orthogroup_size $min_orthogroup_size
--max_orthogroup_size $max_orthogroup_size
--num_threads \${GALAXY_SLOTS:-4}
#set output_pttree_dir = $output_pttree_dir_cond.output_pttree_dir
#if str($output_pttree_dir) == 'yes':
    --output_tree '$output_tree'
    --output_tree_dir '$output_tree.files_path'
#end if
    ]]></command>

            </when>
            <when value="fasttree" />
        </conditional>
        <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
        <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
        <conditional name="output_pttree_dir_cond">
            <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes" />
        </conditional>
    </inputs>
    <outputs>
        <collection name="tree" type="list" label="${tool.name} (phylogenetic trees, dataset collection) on ${on_string}">
            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
        </collection>
        <data name="output_tree" format="pttree" label="${tool.name} (phylogenetic trees, directory) on ${on_string}">
            <filter>output_pttree_dir_cond['output_pttree_dir'] == 'yes'</filter>
        </data>
        <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
            <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
        </data>
    </outputs>

4:1134528b93cc

    --output_phylip_dir '$output_phylip.files_path'
#end if
--min_orthogroup_size $min_orthogroup_size
--max_orthogroup_size $max_orthogroup_size
--num_threads \${GALAXY_SLOTS:-4}
#if str($output_pttree_dir) == 'yes':
    --output_tree '$output_tree'
    --output_tree_dir '$output_tree.files_path'
#end if
    ]]></command>

            </when>
            <when value="fasttree" />
        </conditional>
        <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
        <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
        <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <collection name="tree" type="list" label="${tool.name} (phylogenetic trees, dataset collection) on ${on_string}">
            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
        </collection>
        <data name="output_tree" format="pttree" label="${tool.name} (phylogenetic trees, directory) on ${on_string}">
            <filter>output_pttree_dir == 'yes'</filter>
        </data>
        <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
            <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
        </data>
    </outputs>