Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 18:b14a129fe55f draft

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Uploaded
author greg
date Thu, 05 Jan 2017 14:01:37 -0500
parents cb7487bdab99
children c4a9c23334a4
comparison
equal deleted inserted replaced
17:cb7487bdab99 18:b14a129fe55f
18 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 18 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
19 #set dest_dir = $output.extra_files_path 19 #set dest_dir = $output.extra_files_path
20 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 20 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
21 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 21 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
22 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond 22 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
23 #set create_corresponding_coding_sequences = $create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences 23 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
24 #set create_corresponding_coding_sequences = True
25 #else:
26 #set create_corresponding_coding_sequences = False
27 #endif
24 mkdir -p $dest_dir && 28 mkdir -p $dest_dir &&
25 #else: 29 #else:
26 #set create_ortho_sequences = False 30 #set create_ortho_sequences = False
27 #end if 31 #end if
28 GeneFamilyClassifier 32 GeneFamilyClassifier
36 --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa 40 --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa
37 --taxa_present $options_type.single_copy_cond.taxa_present 41 --taxa_present $options_type.single_copy_cond.taxa_present
38 #end if 42 #end if
39 #if str($create_orthogroup) == 'yes': 43 #if str($create_orthogroup) == 'yes':
40 --orthogroup_fasta 44 --orthogroup_fasta
41 #if $create_corresponding_coding_sequences == 'yes': 45 #if $create_corresponding_coding_sequences:
42 --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences" 46 --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences"
43 #end if 47 #end if
44 #end if 48 #end if
45 #end if 49 #end if
46 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 50 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
51 #else: 55 #else:
52 && rm geneFamilyClassification_dir/hmmscan.log 56 && rm geneFamilyClassification_dir/hmmscan.log
53 #end if 57 #end if
54 #end if 58 #end if
55 #if $create_ortho_sequences: 59 #if $create_ortho_sequences:
56 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output 60 #if $create_corresponding_coding_sequences:
61 && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
62 #else:
63 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
64 #end if
57 && ls $orthogroups_fasta_src_dir >> $output 65 && ls $orthogroups_fasta_src_dir >> $output
58 && mv $orthogroups_fasta_src_dir/* $dest_dir 66 && mv $orthogroups_fasta_src_dir/* $dest_dir
59 #end if 67 #end if
60 ]]> 68 ]]>
61 </command> 69 </command>