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comparison gene_family_classifier.xml @ 3:3e10a2683769 draft

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author greg
date Mon, 30 Oct 2017 09:52:34 -0400
parents 8ec75782a05b
children fd170580a6c9
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2:8ec75782a05b 3:3e10a2683769
1 <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.2"> 1 <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.3.0">
2 <description>classifies gene sequences into pre-computed orthologous gene family clusters</description> 2 <description>classifies gene sequences into pre-computed orthologous gene family clusters</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_gene_family_classifier" /> 6 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_classifier</requirement>
8 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 #if str($options_type.options_type_selector) == 'advanced': 10 #if str($options_type.options_type_selector) == 'advanced':
9 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond 11 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
10 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups 12 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
11 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 13 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
81 #end if 83 #end if
82 #end if 84 #end if
83 85
84 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': 86 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
85 --save_hmmscan_log true 87 --save_hmmscan_log true
86 --hmmscan_log '$hmmscan_log' 88 --hmmscan_log '$output_hmmscan_log'
87 #end if
88 #if $create_ortho_sequences:
89 #if $create_corresponding_coding_sequences:
90 --output_ptorthocs '$output_ptorthocs'
91 --output_ptorthocs_dir '$output_ptorthocs.files_path'
92 #else:
93 --output_ptortho '$output_ptortho'
94 --output_ptortho_dir '$output_ptortho.files_path'
95 #end if
96 #end if
97 #if $single_copy_orthogroup:
98 #if $create_ortho_sequences:
99 --output_ptsco '$output_ptsco'
100 --output_ptsco_dir '$output_ptsco.files_path'
101 #end if
102 #end if 89 #end if
103 ]]></command> 90 ]]></command>
104 <inputs> 91 <inputs>
105 <param name="input" format="fasta" type="data" label="Proteins fasta file"/> 92 <param name="input" format="fasta" type="data" label="Proteins fasta file"/>
106 <param name="scaffold" type="select" label="Gene family scaffold"> 93 <param name="scaffold" type="select" label="Gene family scaffold">
204 </conditional> 191 </conditional>
205 </when> 192 </when>
206 </conditional> 193 </conditional>
207 </inputs> 194 </inputs>
208 <outputs> 195 <outputs>
209 <data name="hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}"> 196 <data name="output_hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}">
210 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> 197 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
211 </data> 198 </data>
212 <data name="output_ptortho" format="ptortho" label="${tool.name} (gene family clusters) on ${on_string}"> 199 <collection name="output_orthos" type="list" label="${tool.name} on ${on_string}">
213 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'no'</filter> 200 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
214 </data> 201 </collection>
215 <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (gene family clusters) on ${on_string}"> 202 <collection name="output_orthogroups_fasta" type="list" label="${tool.name} (gene family clusters) on ${on_string}">
216 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter> 203 <discover_datasets pattern="__name__" directory="output_orthogroups_fasta_dir" visible="false" ext="fasta" />
217 </data> 204 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
218 <data name="output_ptsco" format="tabular" label="${tool.name} (single copy orthogroups) on ${on_string}"> 205 </collection>
206 <collection name="output_single_copy_fasta" type="list" label="${tool.name} (single copy orthogroups) on ${on_string}">
207 <discover_datasets pattern="__name__" directory="output_single_copy_fasta_dir" visible="false" ext="fasta" />
219 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter> 208 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
220 <change_format>
221 <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="no" format="ptortho" />
222 <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="yes" format="ptorthocs" />
223 </change_format>
224 </data>
225 <collection name="orthos" type="list">
226 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
227 </collection> 209 </collection>
228 </outputs> 210 </outputs>
229 <tests> 211 <tests>
230 <test> 212 <test>
231 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta"/> 213 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta"/>
233 <param name="method" value="orthomcl"/> 215 <param name="method" value="orthomcl"/>
234 <param name="classifier" value="both"/> 216 <param name="classifier" value="both"/>
235 <param name="options_type_selector" value="advanced"/> 217 <param name="options_type_selector" value="advanced"/>
236 <param name="create_orthogroup" value="yes"/> 218 <param name="create_orthogroup" value="yes"/>
237 <param name="create_corresponding_coding_sequences" value="yes"/> 219 <param name="create_corresponding_coding_sequences" value="yes"/>
238 <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/> 220 <param name="coding_sequences" value="transcripts.cleaned.nr.cds" ftype="fasta"/>
239 <output_collection name="orthos" type="list"> 221 <output_collection name="output_orthos" type="list">
240 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/> 222 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/>
241 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/> 223 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
242 <element name="proteins.both.22Gv1.1.bestOrthos" file="proteins.both.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/> 224 <element name="proteins.both.22Gv1.1.bestOrthos" file="proteins.both.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
243 <element name="proteins.both.22Gv1.1.bestOrthos.summary" file="proteins.both.22Gv1.1.bestOrthos.summary" ftype="tabular" compare="contains"/> 225 <element name="proteins.both.22Gv1.1.bestOrthos.summary" file="proteins.both.22Gv1.1.bestOrthos.summary" ftype="tabular" compare="contains"/>
244 <element name="proteins.hmmscan.22Gv1.1" file="proteins.hmmscan.22Gv1.1" ftype="tabular" compare="contains"/> 226 <element name="proteins.hmmscan.22Gv1.1" file="proteins.hmmscan.22Gv1.1" ftype="tabular" compare="contains"/>
245 <element name="proteins.hmmscan.22Gv1.1.bestOrthos" file="proteins.hmmscan.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/> 227 <element name="proteins.hmmscan.22Gv1.1.bestOrthos" file="proteins.hmmscan.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
228 </output_collection>
229 <output_collection name="output_orthogroups_fasta" type="list">
230 <element name="20.faa" file="20.faa" ftype="fasta"/>
231 <element name="20.fna" file="20.fna" ftype="fasta"/>
232 <element name="3494.faa" file="3494.faa" ftype="fasta"/>
233 <element name="3494.fna" file="3494.fna" ftype="fasta"/>
234 <element name="3722.faa" file="3722.faa" ftype="fasta"/>
235 <element name="3722.fna" file="3722.fna" ftype="fasta"/>
236 <element name="38889.faa" file="38889.faa" ftype="fasta"/>
237 <element name="38889.fna" file="38889.fna" ftype="fasta"/>
238 <element name="39614.faa" file="39614.faa" ftype="fasta"/>
239 <element name="39614.fna" file="39614.fna" ftype="fasta"/>
240 <element name="5235.faa" file="5235.faa" ftype="fasta"/>
241 <element name="5235.fna" file="5235.fna" ftype="fasta"/>
246 </output_collection> 242 </output_collection>
247 </test> 243 </test>
248 </tests> 244 </tests>
249 <help> 245 <help>
250 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 246 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary