Mercurial > repos > greg > assembly_post_processor
changeset 114:2411671fdc91 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 29 Aug 2018 14:12:28 -0400 |
| parents | 28197cb2d6de |
| children | c625c63bb51a |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 3 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/assembly_post_processor.xml Wed Aug 29 14:12:11 2018 -0400 +++ b/assembly_post_processor.xml Wed Aug 29 14:12:28 2018 -0400 @@ -6,6 +6,7 @@ <requirements> <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement> </requirements> + <code file="get_clustering_methods.py"/> <command detect_errors="exit_code"><![CDATA[ #set output_dir = 'assemblyPostProcessing_dir' AssemblyPostProcessor @@ -92,15 +93,8 @@ <when value="no" /> <when value="yes"> <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/> - <param name="scaffold" type="select" label="Gene family scaffold"> - <options from_data_table="plant_tribes_scaffolds" /> - <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/> - </param> - <param name="method" type="select" label="Protein clustering method"> - <option value="gfam" selected="true">GFam</option> - <option value="orthofinder">OrthoFinder</option> - <option value="orthomcl">OrthoMCL</option> - </param> + <expand macro="param_scaffold"/> + <expand macro="param_method"/> <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/> <param name="min_coverage" type="float" value="0" min="0" max="1.0" label="Minimum alignment coverage"/> </when>