Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 80:32382b0d5add draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 12 Oct 2017 09:52:27 -0400
parents cfb4b150fb3c
children 8378d126347a
comparison
equal deleted inserted replaced
79:03716365973d 80:32382b0d5add
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 '$target_gene_family_assembly_cond.orthogroups'
20 --output_pttgf '$output_pttgf'
21 --output_pttgf_dir '$output_pttgf.files_path'
22 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' 20 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
23 --method '$target_gene_family_assembly_cond.method' 21 --method '$target_gene_family_assembly_cond.method'
24 --gap_trimming $target_gene_family_assembly_cond.gap_trimming 22 --gap_trimming $target_gene_family_assembly_cond.gap_trimming
25 #end if 23 #end if
26 #if str($options_type.strand_specific) == 'yes': 24 #if str($options_type.strand_specific) == 'yes':
89 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/> 87 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
90 </when> 88 </when>
91 </conditional> 89 </conditional>
92 </inputs> 90 </inputs>
93 <outputs> 91 <outputs>
94 <data name="output_pttgf" format="pttgf" 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" />
95 <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>
96 </data> 95 </collection>
97 <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}"/>
98 <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}"/>
99 <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}">
100 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter> 99 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
101 </data> 100 </data>
134 <param name="target_gene_family_assembly" value="yes"/> 133 <param name="target_gene_family_assembly" value="yes"/>
135 <param name="orthogroups" value="target_orthos.ids"/> 134 <param name="orthogroups" value="target_orthos.ids"/>
136 <param name="scaffold" value="22Gv1.1"/> 135 <param name="scaffold" value="22Gv1.1"/>
137 <param name="method" value="orthomcl"/> 136 <param name="method" value="orthomcl"/>
138 <param name="dereplicate" value="yes"/> 137 <param name="dereplicate" value="yes"/>
138 <!--
139 <output name="output_pttgf" file="output.pttgf" ftype="pttgf"/> 139 <output name="output_pttgf" file="output.pttgf" ftype="pttgf"/>
140 -->
140 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/> 141 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/>
141 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/> 142 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/>
142 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/> 143 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/>
143 <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/> 144 <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/>
144 <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/> 145 <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/>