Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 91:a9571ff827b4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 26 Oct 2017 09:17:25 -0400
parents 7dc44a577c88
children 55024e4d84d4
comparison
equal deleted inserted replaced
90:7dc44a577c88 91:a9571ff827b4
19 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 19 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
20 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' 20 --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
21 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' 21 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
22 --method '$target_gene_family_assembly_cond.method' 22 --method '$target_gene_family_assembly_cond.method'
23 --gap_trimming $target_gene_family_assembly_cond.gap_trimming 23 --gap_trimming $target_gene_family_assembly_cond.gap_trimming
24 --min_coverage $target_gene_family_assembly_cond.min_coverage 24 #if $target_gene_family_assembly_cond.min_coverage > 0:
25 --min_coverage $target_gene_family_assembly_cond.min_coverage
26 #end if
25 #end if 27 #end if
26 #if str($options_type.strand_specific) == 'yes': 28 #if str($options_type.strand_specific) == 'yes':
27 --strand_specific true 29 --strand_specific true
28 #end if 30 #end if
29 #if str($options_type.dereplicate) == 'yes': 31 #if str($options_type.dereplicate) == 'yes':
147 <param name="target_gene_family_assembly" value="yes"/> 149 <param name="target_gene_family_assembly" value="yes"/>
148 <param name="orthogroups" value="target_orthos.ids"/> 150 <param name="orthogroups" value="target_orthos.ids"/>
149 <param name="scaffold" value="22Gv1.1"/> 151 <param name="scaffold" value="22Gv1.1"/>
150 <param name="method" value="orthomcl"/> 152 <param name="method" value="orthomcl"/>
151 <param name="dereplicate" value="yes"/> 153 <param name="dereplicate" value="yes"/>
152 <param name="min_coverage" value="0"/>
153 <output_collection name="output_targeted_gene_families" type="list"> 154 <output_collection name="output_targeted_gene_families" type="list">
154 <element name="752.faa" file="752.faa" ftype="fasta"/> 155 <element name="752.faa" file="752.faa" ftype="fasta"/>
155 <element name="752.fasta" file="752.fasta" ftype="fasta"/> 156 <element name="752.fasta" file="752.fasta" ftype="fasta"/>
156 <element name="752.fna" file="752.fna" ftype="fasta"/> 157 <element name="752.fna" file="752.fna" ftype="fasta"/>
157 </output_collection> 158 </output_collection>