Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 25:e6f16430822d draft

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Uploaded
author greg
date Fri, 12 May 2017 09:39:16 -0400
parents 4965a25fa094
children 42da330542c1
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24:61825c063bf3 25:e6f16430822d
52 --rooting_order '$rooting_order' 52 --rooting_order '$rooting_order'
53 ## No else block needed here because the default rooting_order 53 ## No else block needed here because the default rooting_order
54 ## configuration will be used if the --rooting_order flag is missing. 54 ## configuration will be used if the --rooting_order flag is missing.
55 #end if 55 #end if
56 --bootstrap_replicates $bootstrap_replicates 56 --bootstrap_replicates $bootstrap_replicates
57 ##--output_phylip '$output_phylip' 57 --output_phylip '$output_phylip'
58 ##--output_phylip_dir '$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 $max_orthogroup_size
62 --num_threads \${GALAXY_SLOTS:-4} 62 --num_threads \${GALAXY_SLOTS:-4}
63 ##--output_tree '$output_tree'
64 ##--output_tree_dir '$output_tree.files_path'
65 ]]> 63 ]]>
66 </command> 64 </command>
67 <inputs> 65 <inputs>
68 <conditional name="input_format_cond"> 66 <conditional name="input_format_cond">
69 <param name="input_format" type="select" label="Orthogroup alignments"> 67 <param name="input_format" type="select" label="Orthogroup alignments">
132 </conditional> 130 </conditional>
133 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum orthogroup size" /> 131 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum orthogroup size" />
134 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum orthogroup size" /> 132 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum orthogroup size" />
135 </inputs> 133 </inputs>
136 <outputs> 134 <outputs>
137 <collection name="phylip" type="list"> 135 <data name="output_phylip" format="ptphylip" label="Orthogroup phylip multiple sequence alignments on ${on_string}">
138 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" /> 136 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
139 </collection> 137 </data>
140 <collection name="tree" type="list"> 138 <collection name="tree" type="list" label="GeneFamilyPhylogenyBuilder phylogenetic trees on ${on_string}">
141 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" /> 139 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
142 </collection> 140 </collection>
143 </outputs> 141 </outputs>
144 <tests> 142 <tests>
145 <test> 143 <test>