Mercurial > repos > greg > plant_tribes_assembly_post_processor
comparison assembly_post_processor.xml @ 10:4d73965d99a2 draft
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor commit 71ba0e157346927bf42b788f552b95a71556b28a"
author | greg |
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date | Wed, 09 Jun 2021 20:26:55 +0000 |
parents | 9c72c91d291f |
children | 2c2ad8af0a4e |
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9:9c72c91d291f | 10:4d73965d99a2 |
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9 <code file="get_clustering_methods.py"/> | 9 <code file="get_clustering_methods.py"/> |
10 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
11 #set output_dir = 'assemblyPostProcessing_dir' | 11 #set output_dir = 'assemblyPostProcessing_dir' |
12 AssemblyPostProcessor | 12 AssemblyPostProcessor |
13 --transcripts '$input' | 13 --transcripts '$input' |
14 --prediction_method $prediction_method_cond.prediction_method | 14 --prediction_method 'transdecoder' |
15 #if str($prediction_method_cond.prediction_method) == 'estscan': | |
16 --score_matrices '$score_matrices' | |
17 #end if | |
18 #if str($options_type.options_type_selector) == 'advanced': | 15 #if str($options_type.options_type_selector) == 'advanced': |
19 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond | 16 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond |
20 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': | 17 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': |
21 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' | 18 --gene_family_search '$target_gene_family_assembly_cond.orthogroups' |
22 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' | 19 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' |
66 #end if | 63 #end if |
67 #end if | 64 #end if |
68 fi]]></command> | 65 fi]]></command> |
69 <inputs> | 66 <inputs> |
70 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> | 67 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> |
71 <conditional name="prediction_method_cond"> | |
72 <param name="prediction_method" type="select" label="Coding regions prediction method"> | |
73 <option value="transdecoder" selected="true">TransDecoder</option> | |
74 <option value="estscan">ESTScan</option> | |
75 </param> | |
76 <when value="transdecoder" /> | |
77 <when value="estscan"> | |
78 <param name="score_matrices" format="smat" type="data" label="Scores matrices"/> | |
79 </when> | |
80 </conditional> | |
81 <conditional name="options_type"> | 68 <conditional name="options_type"> |
82 <param name="options_type_selector" type="select" label="Options configuration"> | 69 <param name="options_type_selector" type="select" label="Options configuration"> |
83 <option value="basic" selected="true">Basic</option> | 70 <option value="basic" selected="true">Basic</option> |
84 <option value="advanced">Advanced</option> | 71 <option value="advanced">Advanced</option> |
85 </param> | 72 </param> |
131 <data name="output_cds" format="fasta" label="transcripts.cds: ${tool.name} on ${on_string}"/> | 118 <data name="output_cds" format="fasta" label="transcripts.cds: ${tool.name} on ${on_string}"/> |
132 </outputs> | 119 </outputs> |
133 <tests> | 120 <tests> |
134 <test> | 121 <test> |
135 <param name="input" value="assembly.fasta" ftype="fasta"/> | 122 <param name="input" value="assembly.fasta" ftype="fasta"/> |
136 <param name="prediction_method" value="transdecoder"/> | |
137 <output name="output_cds" file="transcripts.cds" ftype="fasta"/> | 123 <output name="output_cds" file="transcripts.cds" ftype="fasta"/> |
138 <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/> | 124 <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/> |
139 <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/> | 125 <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/> |
140 <output name="output_pep" file="transcripts.pep" ftype="fasta"/> | 126 <output name="output_pep" file="transcripts.pep" ftype="fasta"/> |
141 </test> | 127 </test> |
142 <test> | 128 <test> |
143 <param name="input" value="assembly.fasta" ftype="fasta"/> | |
144 <param name="prediction_method" value="estscan"/> | |
145 <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/> | |
146 <param name="options_type_selector" value="advanced"/> | |
147 <param name="dereplicate" value="yes"/> | |
148 <output name="output_cds" file="transcripts2.cds" ftype="fasta"/> | |
149 <output name="output_cleaned_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> | |
150 <output name="output_cleaned_nr_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> | |
151 <output name="output_cleaned_nr_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> | |
152 <output name="output_cleaned_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> | |
153 <output name="output_pep" file="transcripts2.pep" ftype="fasta"/> | |
154 </test> | |
155 <test> | |
156 <param name="input" value="assembly_tgf.fasta" ftype="fasta"/> | 129 <param name="input" value="assembly_tgf.fasta" ftype="fasta"/> |
157 <param name="prediction_method" value="transdecoder"/> | |
158 <param name="options_type_selector" value="advanced"/> | 130 <param name="options_type_selector" value="advanced"/> |
159 <param name="target_gene_family_assembly" value="yes"/> | 131 <param name="target_gene_family_assembly" value="yes"/> |
160 <param name="orthogroups" value="target_orthos.ids"/> | 132 <param name="orthogroups" value="target_orthos.ids"/> |
161 <param name="scaffold" value="22Gv1.1"/> | |
162 <param name="method" value="orthomcl"/> | 133 <param name="method" value="orthomcl"/> |
163 <param name="dereplicate" value="yes"/> | 134 <param name="dereplicate" value="yes"/> |
164 <output_collection name="output_targeted_gene_families" type="list"> | 135 <output_collection name="output_targeted_gene_families" type="list"> |
165 </output_collection> | 136 </output_collection> |
166 <output name="output_targeted_gene_families_stats" file="output_targeted_gene_families_stats.tabular" ftype="tabular"/> | 137 <output name="output_targeted_gene_families_stats" file="output_targeted_gene_families_stats.tabular" ftype="tabular"/> |
184 | 155 |
185 **Required options** | 156 **Required options** |
186 | 157 |
187 * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history. | 158 * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history. |
188 * **Coding regions prediction method** - method for finding coding regions within transcripts. Available methods are TransDecoder[3] and ESTScan[4]. | 159 * **Coding regions prediction method** - method for finding coding regions within transcripts. Available methods are TransDecoder[3] and ESTScan[4]. |
189 * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is used to find coding regions. Details of how to create species-specific scores matrices can be found on the ESTScan website (http://estscan.sourceforge.net). Matrices of some organisms are also available to download. | |
190 | 160 |
191 **Other options** | 161 **Other options** |
192 | 162 |
193 * **Perform targeted gene assembly?** - selecting 'Yes' enables local assembly of one or more targeted gene families in a specific scaffold. Scaffolds are defined in PlantTribes as clusters of paralogous/orthologous sequences from a specified set of proteomes[5-7]. | 163 * **Perform targeted gene assembly?** - selecting 'Yes' enables local assembly of one or more targeted gene families in a specific scaffold. Scaffolds are defined in PlantTribes as clusters of paralogous/orthologous sequences from a specified set of proteomes[5-7]. |
194 | 164 |
222 title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis}, | 192 title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis}, |
223 year = {2013}, | 193 year = {2013}, |
224 volume = {8}, | 194 volume = {8}, |
225 number = {8}, | 195 number = {8}, |
226 pages = {1494-1512},} | 196 pages = {1494-1512},} |
227 </citation> | |
228 <citation type="bibtex"> | |
229 @article{Iseli1999, | |
230 journal = {ISMB}, | |
231 author = {4. Iseli C, Jongeneel CV, Bucher P}, | |
232 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences}, | |
233 year = {1999}, | |
234 volume = {99}, | |
235 pages = {138-148}, | |
236 url = {http://estscan.sourceforge.net},} | |
237 </citation> | 197 </citation> |
238 <citation type="bibtex"> | 198 <citation type="bibtex"> |
239 @article{Huang1999, | 199 @article{Huang1999, |
240 journal = {Genome Research}, | 200 journal = {Genome Research}, |
241 author = {5. Huang X, Madan A}, | 201 author = {5. Huang X, Madan A}, |