Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 78:cfb4b150fb3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 05 Oct 2017 14:11:04 -0400
parents ce5b201b7782
children 32382b0d5add
comparison
equal deleted inserted replaced
77:2849bcb0b7ed 78:cfb4b150fb3c
15 #end if 15 #end if
16 #if str($options_type.options_type_selector) == 'advanced': 16 #if str($options_type.options_type_selector) == 'advanced':
17 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond 17 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
18 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 18 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
19 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' 19 --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
20 --move_stats true 20 --output_pttgf '$output_pttgf'
21 --output_pttgf_dir '$output_pttgf.files_path'
21 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' 22 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
22 --method '$target_gene_family_assembly_cond.method' 23 --method '$target_gene_family_assembly_cond.method'
23 --gap_trimming $target_gene_family_assembly_cond.gap_trimming 24 --gap_trimming $target_gene_family_assembly_cond.gap_trimming
24 #end if 25 #end if
25 #if str($options_type.strand_specific) == 'yes': 26 #if str($options_type.strand_specific) == 'yes':
88 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/> 89 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
89 </when> 90 </when>
90 </conditional> 91 </conditional>
91 </inputs> 92 </inputs>
92 <outputs> 93 <outputs>
93 <collection name="output_stats" type="list" label="Targeted gene families statistics: ${tool.name} on ${on_string}"> 94 <data name="output_pttgf" format="pttgf" label="Targeted gene families: ${tool.name} on ${on_string}">
94 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families_statistics" format="tabular" />
95 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter> 95 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
96 </collection> 96 </data>
97 <collection name="output_tgf" type="list" label="Targeted gene families: ${tool.name} on ${on_string}">
98 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families" format="fasta" />
99 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
100 </collection>
101 <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/> 97 <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/>
102 <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/> 98 <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/>
103 <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}"> 99 <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}">
104 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter> 100 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
105 </data> 101 </data>