Mercurial > repos > greg > assembly_post_processor
changeset 16:1e639e679f61 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 13 Feb 2017 07:40:02 -0500 |
| parents | ff5c714e01d1 |
| children | 63a4a0f127da |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 9 insertions(+), 12 deletions(-) [+] |
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--- a/assembly_post_processor.xml Wed Feb 08 09:13:53 2017 -0500 +++ b/assembly_post_processor.xml Mon Feb 13 07:40:02 2017 -0500 @@ -22,11 +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_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path - #set scaffold_dir = $os.path.split($scaffold_path)[0] - #set scaffold = $os.path.split($scaffold_path)[1] + #set scaffold = $options_type.target_gene_family_assembly_cond.scaffold.fields.path --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups' - --scaffold_dir '$scaffold_dir' --scaffold '$scaffold' --method '$options_type.target_gene_family_assembly_cond.method' #end if @@ -105,7 +102,7 @@ <output_collection name="transcripts" type="list"> <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/> <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/> - <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/> + <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/> <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/> </output_collection> </test> @@ -117,12 +114,12 @@ <param name="dereplicate" value="yes" /> <param name="min_length" value="200" /> <output_collection name="transcripts" type="list"> - <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/> - <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> - <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/> - <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/> - <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/> - <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/> + <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/> + <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/> + <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> + <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> + <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/> + <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/> </output_collection> </test> </tests> @@ -139,7 +136,7 @@ * **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. + * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the [Data Manager PlantTribes Scaffolds Downloader tool](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/4c96b684f0fd). * **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.