Mercurial > repos > greg > gene_family_phylogeny_builder
changeset 20:ab4e77327a05 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 11 May 2017 13:42:24 -0400 |
| parents | f33369f4392a |
| children | 451ad91530b8 |
| files | gene_family_phylogeny_builder.xml |
| diffstat | 1 files changed, 12 insertions(+), 4 deletions(-) [+] |
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--- a/gene_family_phylogeny_builder.xml Wed May 10 14:29:26 2017 -0400 +++ b/gene_family_phylogeny_builder.xml Thu May 11 13:42:24 2017 -0400 @@ -54,14 +54,14 @@ ## 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 '$output_tree.files_path' + ##--output_tree '$output_tree' + ##--output_tree_dir '$output_tree.files_path' ]]> </command> <inputs> @@ -134,10 +134,18 @@ <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum orthogroup size" /> </inputs> <outputs> + <!-- <data name="output_phylip" format="ptphylip" label="Gene family orthogroup phylip multiple sequence alignments on ${on_string}"> <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> </data> <data name="output_tree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" /> + --> + <collection name="phylip" type="list"> + <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" visible="true" ext="fasta" /> + </collection> + <collection name="tree" type="list"> + <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" visible="true" ext="fasta" /> + </collection> </outputs> <tests> <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.