Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 31:80e9d6e098ec draft

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Uploaded
author greg
date Mon, 30 Jan 2017 15:22:06 -0500
parents e9d9632762ca
children 364960a5ad2c
comparison
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30:e9d9632762ca 31:80e9d6e098ec
11 <regex match="Error:" /> 11 <regex match="Error:" />
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #set output_label = ""
17 #if str($options_type.options_type_selector) == 'advanced': 16 #if str($options_type.options_type_selector) == 'advanced':
18 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 17 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
19 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 18 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
20 19
21 #if str($create_orthogroup) == 'yes': 20 #if str($create_orthogroup) == 'yes':
55 --taxa_present $options_type.single_copy_cond.taxa_present 54 --taxa_present $options_type.single_copy_cond.taxa_present
56 #end if 55 #end if
57 #if str($create_orthogroup) == 'yes': 56 #if str($create_orthogroup) == 'yes':
58 --orthogroup_fasta 57 --orthogroup_fasta
59 #if $create_corresponding_coding_sequences: 58 #if $create_corresponding_coding_sequences:
60 #set output_label = "Gene family clusters with corresponding coding sequences"
61 --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences" 59 --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences"
62 #else:
63 #set output_label = "Gene family clusters"
64 #end if 60 #end if
65 #end if 61 #end if
66 #end if 62 #end if
67 63
68 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both': 64 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
162 </inputs> 158 </inputs>
163 <outputs> 159 <outputs>
164 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}"> 160 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
165 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> 161 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
166 </data> 162 </data>
167 <data name="output" format="txt" label="${output_label} on ${on_string}"> 163 <data name="output" format="txt" label="Gene family clusters on ${on_string}">
168 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter> 164 <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>
165 </data>
166 <data name="output" format="txt" label="Gene family clusters and corresponding coding sequences on ${on_string}">
167 <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>
169 </data> 168 </data>
170 <collection name="orthos" type="list"> 169 <collection name="orthos" type="list">
171 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 170 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
172 </collection> 171 </collection>
173 </outputs> 172 </outputs>