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comparison assembly_post_processor.xml @ 55:5c221f721b95 draft

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author greg
date Mon, 22 May 2017 10:12:00 -0400
parents 564163c7afd8
children 3d2aff5a0c07
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54:9a105e8f08e5 55:5c221f721b95
11 --prediction_method $prediction_method_cond.prediction_method 11 --prediction_method $prediction_method_cond.prediction_method
12 #if str($prediction_method_cond.prediction_method) == 'estscan': 12 #if str($prediction_method_cond.prediction_method) == 'estscan':
13 --score_matrices '$score_matrices' 13 --score_matrices '$score_matrices'
14 #end if 14 #end if
15 #if str($options_type.options_type_selector) == 'advanced': 15 #if str($options_type.options_type_selector) == 'advanced':
16 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 16 #if str($) == 'yes':
17 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond 17 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
18 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' 18 --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
19 --output_pttgf $output_pttgf
20 --output_pttgf_dir $output_pttgf.files_path
19 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' 21 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
20 --method '$target_gene_family_assembly_cond.method' 22 --method '$target_gene_family_assembly_cond.method'
21 --gap_trimming $target_gene_family_assembly_cond.gap_trimming 23 --gap_trimming $target_gene_family_assembly_cond.gap_trimming
22 #end if 24 #end if
23 #if str($options_type.strand_specific) == 'yes': 25 #if str($options_type.strand_specific) == 'yes':
81 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/> 83 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
82 </when> 84 </when>
83 </conditional> 85 </conditional>
84 </inputs> 86 </inputs>
85 <outputs> 87 <outputs>
88 <data name="output_pttgf" format="pttgf" label="${tool.name} (targeted gene families) on ${on_string}">
89 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
90 </data>
86 <collection name="transcripts" type="list"> 91 <collection name="transcripts" type="list">
87 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" /> 92 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" />
88 </collection> 93 </collection>
89 </outputs> 94 </outputs>
90 <tests> 95 <tests>
98 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/> 103 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
99 </output_collection> 104 </output_collection>
100 </test> 105 </test>
101 <test> 106 <test>
102 <param name="input" value="assembly.fasta" ftype="fasta" /> 107 <param name="input" value="assembly.fasta" ftype="fasta" />
103 <param name="prediction_method" value="transdecoder" /> 108 <param name="prediction_method" value="estscan" />
109 <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/>
104 <param name="options_type_selector" value="advanced" /> 110 <param name="options_type_selector" value="advanced" />
105 <param name="gap_trimming" value="0.1" />
106 <param name="dereplicate" value="yes" /> 111 <param name="dereplicate" value="yes" />
107 <param name="min_length" value="200" />
108 <output_collection name="transcripts" type="list"> 112 <output_collection name="transcripts" type="list">
109 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/> 113 <element name="transcripts.cds" file="transcripts2.cds" ftype="fasta"/>
110 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/> 114 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
111 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> 115 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
112 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> 116 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
113 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/> 117 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
114 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/> 118 <element name="transcripts.pep" file="transcripts2.pep" ftype="fasta"/>
115 </output_collection> 119 </output_collection>
116 </test> 120 </test>
117 </tests> 121 </tests>
118 <help> 122 <help>
119 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and 123 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and