Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 45:916fb0014f89 draft

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Uploaded
author greg
date Tue, 07 Feb 2017 13:40:58 -0500
parents 46f43a90492a
children 6c3fa9907d9c
comparison
equal deleted inserted replaced
44:46f43a90492a 45:916fb0014f89
29 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta') 29 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
30 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path 30 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
31 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond 31 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
32 ## FixMe: the single_copy_custom option is not currently supported. 32 ## FixMe: the single_copy_custom option is not currently supported.
33 #set single_copy = $single_copy_cond.single_copy 33 #set single_copy = $single_copy_cond.single_copy
34
35 mkdir -p $single_copy_fasta_dest_dir && 34 mkdir -p $single_copy_fasta_dest_dir &&
36 #else: 35 #else:
37 #set specify_single_copy = False 36 #set specify_single_copy = False
38 #end if 37 #end if
39 38
42 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 41 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
43 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond 42 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
44 43
45 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': 44 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
46 #set create_corresponding_coding_sequences = True 45 #set create_corresponding_coding_sequences = True
46 #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path
47 #else: 47 #else:
48 #set create_corresponding_coding_sequences = False 48 #set create_corresponding_coding_sequences = False
49 #end if
50
51 #if $create_corresponding_coding_sequences:
52 #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path
53 #else:
54 #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path 49 #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path
55 #end if 50 #end if
56
57 mkdir -p $orthogroups_fasta_dest_dir && 51 mkdir -p $orthogroups_fasta_dest_dir &&
58 #else: 52 #else:
59 #set create_ortho_sequences = False 53 #set create_ortho_sequences = False
60 #set create_corresponding_coding_sequences = False 54 #set create_corresponding_coding_sequences = False
61 #end if 55 #end if
62 #else: 56 #else:
57 #set specify_single_copy = False
63 #set create_ortho_sequences = False 58 #set create_ortho_sequences = False
64 #set create_corresponding_coding_sequences = False 59 #set create_corresponding_coding_sequences = False
65 #end if 60 #end if
66 61
67 GeneFamilyClassifier 62 GeneFamilyClassifier
95 #end if 90 #end if
96 #end if 91 #end if
97 92
98 #if $create_ortho_sequences: 93 #if $create_ortho_sequences:
99 #if $create_corresponding_coding_sequences: 94 #if $create_corresponding_coding_sequences:
100 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgfcs 95 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
101 #else: 96 #else:
102 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgf 97 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
103 #end if 98 #end if
104 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true 99 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
105 #end if 100 #end if
106 101
107 #if $specify_single_copy: 102 #if $specify_single_copy:
108 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco 103 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
109 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true 104 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
110 #end if 105 #end if
111 ]]> 106 ]]>
112 </command> 107 </command>
113 <inputs> 108 <inputs>
208 <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> 203 <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>
209 </data> 204 </data>
210 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}"> 205 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
211 <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> 206 <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>
212 </data> 207 </data>
213 <data name="output_ptsco" format="ptsco" label="Single copy orthogroup on ${on_string}"> 208 <data name="output_ptsco" format="txt" label="Single copy orthogroup on ${on_string}">
214 <filter>options_type['options_type_selector'] == 'advanced' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter> 209 <filter>options_type['options_type_selector'] == 'advanced' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
215 </data> 210 </data>
216 <collection name="orthos" type="list"> 211 <collection name="orthos" type="list">
217 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 212 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
218 </collection> 213 </collection>
253 248
254 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 249 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
255 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 250 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
256 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive). 251 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
257 * **Super Orthogroups** - Secondary MCL clusters of orthogroups. 252 * **Super Orthogroups** - Secondary MCL clusters of orthogroups.
253 * **Specify single copy orthogroup selection?** - Select 'Yes' to specify one of 'Single copy orthogroup custom' (not yet supported) or 'Minumum single copy taxa required in orthogroup'.
258 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. 254 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
259 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. 255 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
260 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?". 256 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
261 257
262 </help> 258 </help>