Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 87:e8d7d4a1672f draft

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Uploaded
author greg
date Wed, 25 Oct 2017 09:13:54 -0400
parents 126430ebebf7
children a9ca872be416
comparison
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86:126430ebebf7 87:e8d7d4a1672f
30 --dereplicate true 30 --dereplicate true
31 #end if 31 #end if
32 --min_length $options_type.min_length 32 --min_length $options_type.min_length
33 #end if 33 #end if
34 --num_threads \${GALAXY_SLOTS:-4} 34 --num_threads \${GALAXY_SLOTS:-4}
35 2>&1
35 && mv $output_dir/transcripts.cds '$output_cds' 36 && mv $output_dir/transcripts.cds '$output_cds'
36 && mv $output_dir/transcripts.pep '$output_pep' 37 && mv $output_dir/transcripts.pep '$output_pep'
37 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' 38 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
38 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' 39 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
39 #if str($options_type.options_type_selector) == 'advanced': 40 #if str($options_type.options_type_selector) == 'advanced':
146 <param name="target_gene_family_assembly" value="yes"/> 147 <param name="target_gene_family_assembly" value="yes"/>
147 <param name="orthogroups" value="target_orthos.ids"/> 148 <param name="orthogroups" value="target_orthos.ids"/>
148 <param name="scaffold" value="22Gv1.1"/> 149 <param name="scaffold" value="22Gv1.1"/>
149 <param name="method" value="orthomcl"/> 150 <param name="method" value="orthomcl"/>
150 <param name="dereplicate" value="yes"/> 151 <param name="dereplicate" value="yes"/>
152 <param name="min_coverage" value="0.3"/>
151 <output_collection name="output_targeted_gene_families" type="list"> 153 <output_collection name="output_targeted_gene_families" type="list">
152 <element name="752.faa" file="752.faa" ftype="fasta"/> 154 <element name="752.faa" file="752.faa" ftype="fasta"/>
153 <element name="752.fasta" file="752.fasta" ftype="fasta"/> 155 <element name="752.fasta" file="752.fasta" ftype="fasta"/>
154 <element name="752.fna" file="752.fna" ftype="fasta"/> 156 <element name="752.fna" file="752.fna" ftype="fasta"/>
155 </output_collection> 157 </output_collection>