Mercurial > repos > greg > gene_family_phylogeny_builder
changeset 25:e6f16430822d draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 12 May 2017 09:39:16 -0400 |
| parents | 61825c063bf3 |
| children | 42da330542c1 |
| files | gene_family_phylogeny_builder.xml |
| diffstat | 1 files changed, 6 insertions(+), 8 deletions(-) [+] |
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--- a/gene_family_phylogeny_builder.xml Fri May 12 09:39:06 2017 -0400 +++ b/gene_family_phylogeny_builder.xml Fri May 12 09:39:16 2017 -0400 @@ -54,14 +54,12 @@ ## configuration will be used if the --rooting_order flag is missing. #end if --bootstrap_replicates $bootstrap_replicates - ##--output_phylip '$output_phylip' - ##--output_phylip_dir '$output_phylip.files_path' + --output_phylip '$output_phylip' + --output_phylip_dir '$output_phylip.files_path' #end if --min_orthogroup_size $min_orthogroup_size --max_orthogroup_size $max_orthogroup_size --num_threads \${GALAXY_SLOTS:-4} - ##--output_tree '$output_tree' - ##--output_tree_dir '$output_tree.files_path' ]]> </command> <inputs> @@ -134,10 +132,10 @@ <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum orthogroup size" /> </inputs> <outputs> - <collection name="phylip" type="list"> - <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" /> - </collection> - <collection name="tree" type="list"> + <data name="output_phylip" format="ptphylip" label="Orthogroup phylip multiple sequence alignments on ${on_string}"> + <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> + </data> + <collection name="tree" type="list" label="GeneFamilyPhylogenyBuilder phylogenetic trees on ${on_string}"> <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" /> </collection> </outputs>