Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 44:46f43a90492a draft

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author greg
date Tue, 07 Feb 2017 11:48:18 -0500
parents 8d1dbff42659
children 916fb0014f89
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43:8d1dbff42659 44:46f43a90492a
19 #set scaffold_selection = $os.path.split($scaffold_path)[1] 19 #set scaffold_selection = $os.path.split($scaffold_path)[1]
20 20
21 #if str($options_type.options_type_selector) == 'advanced': 21 #if str($options_type.options_type_selector) == 'advanced':
22 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 22 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
23 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 23 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
24 #set specify_single_copy_cond = $options_type.specify_single_copy_cond
25 #set specify_single_copy = $specify_single_copy_cond.single_copy_cond
26
27 #if str($specify_single_copy) == 'yes':
28 #set specify_single_copy = True
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
31 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
32 ## FixMe: the single_copy_custom option is not currently supported.
33 #set single_copy = $single_copy_cond.single_copy
34
35 mkdir -p $single_copy_fasta_dest_dir &&
36 #else:
37 #set specify_single_copy = False
38 #end if
24 39
25 #if str($create_orthogroup) == 'yes': 40 #if str($create_orthogroup) == 'yes':
41 #set create_ortho_sequences = True
42 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
26 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond 43 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
44
27 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': 45 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
28 #set create_corresponding_coding_sequences = True 46 #set create_corresponding_coding_sequences = True
29 #else: 47 #else:
30 #set create_corresponding_coding_sequences = False 48 #set create_corresponding_coding_sequences = False
31 #end if 49 #end if
32 50
33 #set create_ortho_sequences = True
34 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
35 #if $create_corresponding_coding_sequences: 51 #if $create_corresponding_coding_sequences:
36 #set dest_dir = $output_ptcgfcs.extra_files_path 52 #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path
37 #else: 53 #else:
38 #set dest_dir = $output_ptcgf.extra_files_path 54 #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path
39 #end if 55 #end if
40 mkdir -p $dest_dir && 56
57 mkdir -p $orthogroups_fasta_dest_dir &&
41 #else: 58 #else:
42 #set create_ortho_sequences = False 59 #set create_ortho_sequences = False
43 #set create_corresponding_coding_sequences = False 60 #set create_corresponding_coding_sequences = False
44 #end if 61 #end if
45 #else: 62 #else:
55 --classifier $save_hmmscan_log_cond.classifier 72 --classifier $save_hmmscan_log_cond.classifier
56 --num_threads \${GALAXY_SLOTS:-4} 73 --num_threads \${GALAXY_SLOTS:-4}
57 74
58 #if str($options_type.options_type_selector) == 'advanced': 75 #if str($options_type.options_type_selector) == 'advanced':
59 --super_orthogroups $options_type.super_orthogroups 76 --super_orthogroups $options_type.super_orthogroups
60 #if str($options_type.single_copy_cond) == 'taxa': 77 #if $specify_single_copy:
61 --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa 78 --single_copy_taxa $single_copy_cond.single_copy_taxa
62 --taxa_present $options_type.single_copy_cond.taxa_present 79 --taxa_present $single_copy_cond.taxa_present
63 #end if 80 #end if
64 #if str($create_orthogroup) == 'yes': 81 #if str($create_orthogroup) == 'yes':
65 --orthogroup_fasta 82 --orthogroup_fasta
66 #if $create_corresponding_coding_sequences: 83 #if $create_corresponding_coding_sequences:
67 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences' 84 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences'
68 #end if 85 #end if
69 #end if 86 #end if
70 #end if 87 #end if
88 >/dev/null
71 89
72 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both': 90 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
73 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': 91 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
74 && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log 92 && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log
75 #else: 93 #else:
77 #end if 95 #end if
78 #end if 96 #end if
79 97
80 #if $create_ortho_sequences: 98 #if $create_ortho_sequences:
81 #if $create_corresponding_coding_sequences: 99 #if $create_corresponding_coding_sequences:
82 && echo "#Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgfcs 100 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgfcs
83 && echo -e "#Size\t\tFile" >> $output_ptcgfcs 101 #else:
84 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t\t"$9}' >> $output_ptcgfcs 102 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgf
85 #else: 103 #end if
86 && echo "#Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgf 104 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
87 && echo -e "#Size\t\tFile" >> $output_ptcgf 105 #end if
88 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t\t"$9}' >> $output_ptcgf 106
89 #end if 107 #if $specify_single_copy:
90 && mv $orthogroups_fasta_src_dir/* $dest_dir || true 108 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
91 #end if 109 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
92 110 #end if
93 ]]> 111 ]]>
94 </command> 112 </command>
95 <inputs> 113 <inputs>
96 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> 114 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
97 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 115 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
132 <when value="advanced"> 150 <when value="advanced">
133 <param name="super_orthogroups" type="select" label="Super Orthogroups" help="Secondary MCL clusters of orthogroups"> 151 <param name="super_orthogroups" type="select" label="Super Orthogroups" help="Secondary MCL clusters of orthogroups">
134 <option value="min_evalue" selected="true">Minimum e-value</option> 152 <option value="min_evalue" selected="true">Minimum e-value</option>
135 <option value="avg_evalue">Average e-value</option> 153 <option value="avg_evalue">Average e-value</option>
136 </param> 154 </param>
137 <conditional name="single_copy_cond"> 155 <conditional name="specify_single_copy_cond">
138 <param name="single_copy" type="select" label="Select single copy configuration"> 156 <param name="specify_single_copy" type="select" label="Specify single copy orthogroup selection?">
139 <option value="custom" selected="true">Single copy orthogroup custom</option> 157 <option value="no" selected="true">No</option>
140 <option value="taxa">Minumum single copy taxa required in orthogroup</option> 158 <option value="yes">Yes</option>
141 </param> 159 </param>
142 <when value="custom" /> 160 <when value="no"/>
143 <when value="taxa"> 161 <when value="yes">
144 <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/> 162 <conditional name="single_copy_cond">
145 <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/> 163 <param name="single_copy" type="select" label="Select single copy configuration">
164 <!--
165 FixMe: single_copy_custom is not currently supported because the
166 ~/config/*.singleCopy.config files are not easy to manage by a suer
167 and the GeneFamilyClassifier pipeline must be enhanced to provide an
168 optional parameter for the hard-coded path to the config.
169 <option value="custom" selected="true">Single copy orthogroup custom</option>
170 -->
171 <option value="taxa">Minumum single copy taxa required in orthogroup</option>
172 </param>
173 <when value="custom" />
174 <when value="taxa">
175 <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/>
176 <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/>
177 </when>
178 </conditional>
146 </when> 179 </when>
147 </conditional> 180 </conditional>
148 <conditional name="create_orthogroup_cond"> 181 <conditional name="create_orthogroup_cond">
149 <param name="create_orthogroup" type="select" label="Create orthogroup fasta files?"> 182 <param name="create_orthogroup" type="select" label="Create orthogroup fasta files?">
150 <option value="no" selected="true">No</option> 183 <option value="no" selected="true">No</option>
175 <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> 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>
176 </data> 209 </data>
177 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}"> 210 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
178 <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> 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>
179 </data> 212 </data>
213 <data name="output_ptsco" format="ptsco" 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>
215 </data>
180 <collection name="orthos" type="list"> 216 <collection name="orthos" type="list">
181 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 217 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
182 </collection> 218 </collection>
183 </outputs> 219 </outputs>
184 <tests> 220 <tests>