Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 34:9a60634252fd draft

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Uploaded
author greg
date Wed, 01 Feb 2017 15:01:19 -0500
parents c1a3b77de0f0
children 0fc60c5cb719
comparison
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33:c1a3b77de0f0 34:9a60634252fd
26 #end if 26 #end if
27 27
28 #import os 28 #import os
29 #set create_ortho_sequences = True 29 #set create_ortho_sequences = True
30 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 30 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
31 #set dest_dir = $output.extra_files_path 31 #if $create_corresponding_coding_sequences:
32 #set dest_dir = $output_pgfccs.extra_files_path
33 #else:
34 #set dest_dir = $output_pgfc.extra_files_path
35 #end if
32 mkdir -p $dest_dir && 36 mkdir -p $dest_dir &&
33 #else: 37 #else:
34 #set create_ortho_sequences = False 38 #set create_ortho_sequences = False
35 #set create_corresponding_coding_sequences = False 39 #set create_corresponding_coding_sequences = False
36 #end if 40 #end if
69 #end if 73 #end if
70 #end if 74 #end if
71 75
72 #if $create_ortho_sequences: 76 #if $create_ortho_sequences:
73 #if $create_corresponding_coding_sequences: 77 #if $create_corresponding_coding_sequences:
74 && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output 78 && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfccs
79 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfccs
75 #else: 80 #else:
76 && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output 81 && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfc
77 #end if 82 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfc
78 && ls -al $orthogroups_fasta_src_dir | grep f >> $output 83 #end if
79 && mv $orthogroups_fasta_src_dir/* $dest_dir || true 84 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
80 #end if 85 #end if
81 86
82 ]]> 87 ]]>
83 </command> 88 </command>
158 </inputs> 163 </inputs>
159 <outputs> 164 <outputs>
160 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}"> 165 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
161 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> 166 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
162 </data> 167 </data>
163 <data name="output" format="pgfc" label="Gene family clusters on ${on_string}"> 168 <data name="output_pgfc" format="pgfc" label="Gene family clusters on ${on_string}">
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> 169 <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> 170 </data>
166 <data name="output" format="pgfccs" label="Gene family clusters and corresponding coding sequences on ${on_string}"> 171 <data name="output_pgfccs" format="pgfccs" 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> 172 <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>
168 </data> 173 </data>
169 <collection name="orthos" type="list"> 174 <collection name="orthos" type="list">
170 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 175 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
171 </collection> 176 </collection>