Mercurial > repos > greg > assembly_post_processor
changeset 21:913c3e0354cc draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 13 Feb 2017 07:59:49 -0500 |
| parents | 37abc8473df1 |
| children | 9744a653d503 |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 2 insertions(+), 3 deletions(-) [+] |
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--- a/assembly_post_processor.xml Mon Feb 13 07:49:14 2017 -0500 +++ b/assembly_post_processor.xml Mon Feb 13 07:59:49 2017 -0500 @@ -22,9 +22,8 @@ #end if #if str($options_type.options_type_selector) == 'advanced': #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': - #set scaffold = $options_type.target_gene_family_assembly_cond.scaffold.fields.path --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups' - --scaffold '$scaffold' + --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path' --method '$options_type.target_gene_family_assembly_cond.method' #end if --gap_trimming $options_type.gap_trimming @@ -136,7 +135,7 @@ * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms. * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble. * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble. - * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the Data Manager PlantTribes Scaffolds Downloader tool. + * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data, installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool. * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0] * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.