Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 82:8378d126347a draft

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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"/>