Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 29:3d78d366dfcc draft

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author greg
date Fri, 12 May 2017 14:14:19 -0400
parents 6374c987b4a8
children a456fb4d1d44
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28:62fe699992a5 29:3d78d366dfcc
58 --output_phylip_dir '$output_phylip.files_path' 58 --output_phylip_dir '$output_phylip.files_path'
59 #end if 59 #end if
60 --min_orthogroup_size $min_orthogroup_size 60 --min_orthogroup_size $min_orthogroup_size
61 --max_orthogroup_size $max_orthogroup_size 61 --max_orthogroup_size $max_orthogroup_size
62 --num_threads \${GALAXY_SLOTS:-4} 62 --num_threads \${GALAXY_SLOTS:-4}
63 #set output_pttree_dir = output_pttree_dir_cond.output_pttree_dir
64 #if str($output_pttree_dir) == 'yes':
65 --output_tree '$output_tree'
66 --output_tree_dir '$output_tree.files_path'
67 #end if
63 ]]> 68 ]]>
64 </command> 69 </command>
65 <inputs> 70 <inputs>
66 <conditional name="input_format_cond"> 71 <conditional name="input_format_cond">
67 <param name="input_format" type="select" label="Orthogroup alignments"> 72 <param name="input_format" type="select" label="Orthogroup alignments">
128 </when> 133 </when>
129 <when value="fasttree" /> 134 <when value="fasttree" />
130 </conditional> 135 </conditional>
131 <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" /> 136 <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
132 <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" /> 137 <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
138 <conditional name="output_pttree_dir_cond">
139 <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?">
140 <option value="no" selected="true">No</option>
141 <option value="yes">Yes</option>
142 </param>
143 <when value="no" />
144 <when value="yes" />
145 </conditional>
133 </inputs> 146 </inputs>
134 <outputs> 147 <outputs>
148 <collection name="tree" type="list" label="GeneFamilyPhylogenyBuilder phylogenetic trees (dataset collection) on ${on_string}">
149 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
150 </collection>
151 <data name="output_tree" format="pttree" label="GeneFamilyPhylogenyBuilder phylogenetic trees (directory) on ${on_string}">
152 <filter>output_pttree_dir_cond['output_pttree_dir'] == 'yes'</filter>
153 </data>
135 <data name="output_phylip" format="ptphylip" label="GeneFamilyPhylogenyBuilder orthogroup phylip multiple sequence alignments on ${on_string}"> 154 <data name="output_phylip" format="ptphylip" label="GeneFamilyPhylogenyBuilder orthogroup phylip multiple sequence alignments on ${on_string}">
136 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> 155 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
137 </data> 156 </data>
138 <collection name="tree" type="list" label="GeneFamilyPhylogenyBuilder phylogenetic trees on ${on_string}">
139 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
140 </collection>
141 </outputs> 157 </outputs>
142 <tests> 158 <tests>
143 <test> 159 <test>
144 </test> 160 </test>
145 </tests> 161 </tests>