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comparison gene_family_classifier.xml @ 154:36ed0037292a draft

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Uploaded
author greg
date Wed, 04 Oct 2017 13:48:14 -0400
parents 889d928f16b9
children d5a922f09cb9
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153:889d928f16b9 154:36ed0037292a
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 <expand macro="requirements_gene_family_classifier" />
82 #end if 82 #end if
83 83
84 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': 84 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
85 --save_hmmscan_log true 85 --save_hmmscan_log true
86 --hmmscan_log '$hmmscan_log' 86 --hmmscan_log '$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 '$output_ptsco.files_path'
101 #end if
102 #end if 87 #end if
103 ]]></command> 88 ]]></command>
104 <inputs> 89 <inputs>
105 <param name="input" format="fasta" type="data" label="Proteins fasta file"/> 90 <param name="input" format="fasta" type="data" label="Proteins fasta file"/>
106 <param name="scaffold" type="select" label="Gene family scaffold"> 91 <param name="scaffold" type="select" label="Gene family scaffold">
204 </conditional> 189 </conditional>
205 </when> 190 </when>
206 </conditional> 191 </conditional>
207 </inputs> 192 </inputs>
208 <outputs> 193 <outputs>
209 <data name="hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}"> 194 <data name="output_hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}">
210 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> 195 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
211 </data> 196 </data>
212 <data name="output_ptortho" format="ptortho" label="${tool.name} (gene family clusters) on ${on_string}"> 197 <collection name="output_orthos" type="list">
213 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'no'</filter> 198 <discover_datasets pattern="__name__" directory="output_orthos_dir" visible="false" ext="tabular" />
214 </data> 199 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
215 <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (gene family clusters) on ${on_string}"> 200 </collection>
216 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter> 201 <collection name="output_single_copy_fasta" type="list">
217 </data> 202 <discover_datasets pattern="__name__" directory="output_single_copy_fasta_dir" visible="false" ext="fasta" />
218 <data name="output_ptsco" format="tabular" label="${tool.name} (single copy orthogroups) on ${on_string}">
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> 203 <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> 204 </collection>
228 </outputs> 205 </outputs>
229 <tests> 206 <tests>
230 <test> 207 <test>
231 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta"/> 208 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta"/>