Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 4:1134528b93cc draft

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author greg
date Fri, 25 Aug 2017 13:01:04 -0400
parents d939b663bf62
children 34ca28db0a5d
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3:d939b663bf62 4:1134528b93cc
57 --output_phylip_dir '$output_phylip.files_path' 57 --output_phylip_dir '$output_phylip.files_path'
58 #end if 58 #end if
59 --min_orthogroup_size $min_orthogroup_size 59 --min_orthogroup_size $min_orthogroup_size
60 --max_orthogroup_size $max_orthogroup_size 60 --max_orthogroup_size $max_orthogroup_size
61 --num_threads \${GALAXY_SLOTS:-4} 61 --num_threads \${GALAXY_SLOTS:-4}
62 #set output_pttree_dir = $output_pttree_dir_cond.output_pttree_dir
63 #if str($output_pttree_dir) == 'yes': 62 #if str($output_pttree_dir) == 'yes':
64 --output_tree '$output_tree' 63 --output_tree '$output_tree'
65 --output_tree_dir '$output_tree.files_path' 64 --output_tree_dir '$output_tree.files_path'
66 #end if 65 #end if
67 ]]></command> 66 ]]></command>
131 </when> 130 </when>
132 <when value="fasttree" /> 131 <when value="fasttree" />
133 </conditional> 132 </conditional>
134 <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" /> 133 <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
135 <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" /> 134 <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
136 <conditional name="output_pttree_dir_cond"> 135 <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?">
137 <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?"> 136 <option value="no" selected="true">No</option>
138 <option value="no" selected="true">No</option> 137 <option value="yes">Yes</option>
139 <option value="yes">Yes</option> 138 </param>
140 </param>
141 <when value="no" />
142 <when value="yes" />
143 </conditional>
144 </inputs> 139 </inputs>
145 <outputs> 140 <outputs>
146 <collection name="tree" type="list" label="${tool.name} (phylogenetic trees, dataset collection) on ${on_string}"> 141 <collection name="tree" type="list" label="${tool.name} (phylogenetic trees, dataset collection) on ${on_string}">
147 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" /> 142 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
148 </collection> 143 </collection>
149 <data name="output_tree" format="pttree" label="${tool.name} (phylogenetic trees, directory) on ${on_string}"> 144 <data name="output_tree" format="pttree" label="${tool.name} (phylogenetic trees, directory) on ${on_string}">
150 <filter>output_pttree_dir_cond['output_pttree_dir'] == 'yes'</filter> 145 <filter>output_pttree_dir == 'yes'</filter>
151 </data> 146 </data>
152 <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}"> 147 <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
153 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> 148 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
154 </data> 149 </data>
155 </outputs> 150 </outputs>