Mercurial > repos > greg > assembly_post_processor
comparison assembly_post_processor.xml @ 82:8378d126347a draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 12 Oct 2017 10:06:25 -0400 |
| parents | 32382b0d5add |
| children | b1102f939fdd |
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| 81:1a216a9837c7 | 82:8378d126347a |
|---|---|
| 88 </when> | 88 </when> |
| 89 </conditional> | 89 </conditional> |
| 90 </inputs> | 90 </inputs> |
| 91 <outputs> | 91 <outputs> |
| 92 <collection name="output_targeted_gene_families" type="list" label="Targeted gene families: ${tool.name} on ${on_string}"> | 92 <collection name="output_targeted_gene_families" type="list" label="Targeted gene families: ${tool.name} on ${on_string}"> |
| 93 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families" format="fasta" /> | 93 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_family_assemblies" format="fasta" /> |
| 94 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter> | 94 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter> |
| 95 </collection> | 95 </collection> |
| 96 <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/> | 96 <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/> |
| 97 <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/> | 97 <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/> |
| 98 <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}"> | 98 <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}"> |
| 133 <param name="target_gene_family_assembly" value="yes"/> | 133 <param name="target_gene_family_assembly" value="yes"/> |
| 134 <param name="orthogroups" value="target_orthos.ids"/> | 134 <param name="orthogroups" value="target_orthos.ids"/> |
| 135 <param name="scaffold" value="22Gv1.1"/> | 135 <param name="scaffold" value="22Gv1.1"/> |
| 136 <param name="method" value="orthomcl"/> | 136 <param name="method" value="orthomcl"/> |
| 137 <param name="dereplicate" value="yes"/> | 137 <param name="dereplicate" value="yes"/> |
| 138 <!-- | 138 <output_collection name="output_targeted_gene_families" type="list"> |
| 139 <output name="output_pttgf" file="output.pttgf" ftype="pttgf"/> | 139 <element name="752.faa" file="752.faa" ftype="fasta"/> |
| 140 --> | 140 <element name="752.fasta" file="752.fasta" ftype="fasta"/> |
| 141 <element name="752.fna" file="752.fna" ftype="fasta"/> | |
| 142 </output_collection> | |
| 141 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/> | 143 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/> |
| 142 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/> | 144 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/> |
| 143 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/> | 145 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/> |
| 144 <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/> | 146 <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/> |
| 145 <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/> | 147 <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/> |