Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 35:0fc60c5cb719 draft

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author greg
date Thu, 02 Feb 2017 10:06:11 -0500
parents 9a60634252fd
children d485da50616b
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34:9a60634252fd 35:0fc60c5cb719
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 #import os
17 #set scaffold_path = $scaffold.fields.path
18 #set scaffold_dir = $os.path.split($scaffold_path)[0]
19 #set scaffold_selection = $os.path.split($scaffold_path)[1]
20
16 #if str($options_type.options_type_selector) == 'advanced': 21 #if str($options_type.options_type_selector) == 'advanced':
17 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 22 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
18 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 23 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
19 24
20 #if str($create_orthogroup) == 'yes': 25 #if str($create_orthogroup) == 'yes':
23 #set create_corresponding_coding_sequences = True 28 #set create_corresponding_coding_sequences = True
24 #else: 29 #else:
25 #set create_corresponding_coding_sequences = False 30 #set create_corresponding_coding_sequences = False
26 #end if 31 #end if
27 32
28 #import os
29 #set create_ortho_sequences = True 33 #set create_ortho_sequences = True
30 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 34 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
31 #if $create_corresponding_coding_sequences: 35 #if $create_corresponding_coding_sequences:
32 #set dest_dir = $output_pgfccs.extra_files_path 36 #set dest_dir = $output_pgfccs.extra_files_path
33 #else: 37 #else:
42 #set create_ortho_sequences = False 46 #set create_ortho_sequences = False
43 #set create_corresponding_coding_sequences = False 47 #set create_corresponding_coding_sequences = False
44 #end if 48 #end if
45 49
46 GeneFamilyClassifier 50 GeneFamilyClassifier
47 --proteins "$input" 51 --proteins '$input'
48 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 52 --scaffold_dir '$scaffold_dir'
49 --scaffold "$scaffold" 53 --scaffold '$scaffold_selection'
50 --method $method 54 --method $method
51 --classifier $save_hmmscan_log_cond.classifier 55 --classifier $save_hmmscan_log_cond.classifier
52 --num_threads \${GALAXY_SLOTS:-4} 56 --num_threads \${GALAXY_SLOTS:-4}
53 57
54 #if str($options_type.options_type_selector) == 'advanced': 58 #if str($options_type.options_type_selector) == 'advanced':
58 --taxa_present $options_type.single_copy_cond.taxa_present 62 --taxa_present $options_type.single_copy_cond.taxa_present
59 #end if 63 #end if
60 #if str($create_orthogroup) == 'yes': 64 #if str($create_orthogroup) == 'yes':
61 --orthogroup_fasta 65 --orthogroup_fasta
62 #if $create_corresponding_coding_sequences: 66 #if $create_corresponding_coding_sequences:
63 --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences" 67 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences'
64 #end if 68 #end if
65 #end if 69 #end if
66 #end if 70 #end if
67 71
68 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both': 72 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
73 #end if 77 #end if
74 #end if 78 #end if
75 79
76 #if $create_ortho_sequences: 80 #if $create_ortho_sequences:
77 #if $create_corresponding_coding_sequences: 81 #if $create_corresponding_coding_sequences:
78 && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfccs 82 && 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 83 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfccs
80 #else: 84 #else:
81 && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfc 85 && echo '# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files' > $output_pgfc
82 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfc 86 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfc
83 #end if 87 #end if
84 && mv $orthogroups_fasta_src_dir/* $dest_dir || true 88 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
85 #end if 89 #end if
86 90
174 <collection name="orthos" type="list"> 178 <collection name="orthos" type="list">
175 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 179 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
176 </collection> 180 </collection>
177 </outputs> 181 </outputs>
178 <tests> 182 <tests>
183 <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager -->
184 <!--
179 <test> 185 <test>
180 <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager -->
181 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" /> 186 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" />
182 <param name="scaffold" value="22Gv1.1"/> 187 <param name="scaffold" value="22Gv1.1"/>
183 <param name="method" value="orthomcl"/> 188 <param name="method" value="orthomcl"/>
184 <param name="classifier" value="blastp"/> 189 <param name="classifier" value="blastp"/>
185 <param name="dereplicate" value="yes"/> 190 <param name="dereplicate" value="yes"/>
186 <param name="min_length" value="200"/> 191 <param name="min_length" value="200"/>
187 <output_collection name="orthos" type="list"> 192 <output_collection name="orthos" type="list">
188 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/> 193 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular"/>
189 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/> 194 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular"/>
190 <element name="proteins.blastp.22Gv1.1.bestOrthos.summary" file="proteins.blastp.22Gv1.1.bestOrthos.summary" ftype="tabular" compare="contains"/> 195 <element name="proteins.blastp.22Gv1.1.bestOrthos.summary" file="proteins.blastp.22Gv1.1.bestOrthos.summary" ftype="tabular"/>
191 </output_collection> 196 </output_collection>
192 </test> 197 </test>
198 -->
193 </tests> 199 </tests>
194 <help> 200 <help>
195 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 201 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
196 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. This tool classifies gene 202 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. This tool classifies gene
197 sequences into precomputed orthologous gene family clusters using either blastp (faster), HMMScan (slower but more sensitive 203 sequences into precomputed orthologous gene family clusters using either blastp (faster), HMMScan (slower but more sensitive
220 <citation type="bibtex"> 226 <citation type="bibtex">
221 @unpublished{None, 227 @unpublished{None,
222 author = {Eric Wafula}, 228 author = {Eric Wafula},
223 title = {None}, 229 title = {None},
224 year = {None}, 230 year = {None},
225 eprint = {None}, 231 url = {https://github.com/dePamphilis/PlantTribes}
226 url = {None} 232 }</citation>
233 <citation type="doi">10.1186/1471-2105-10-421</citation>
234 <citation type="bibtex">
235 @unpublished{None,
236 author = {None},
237 title = {HMMER 3.1+ hmmscan search sequence(s) against a profile database},
238 year = {2013},
239 url = {http://hmmer.org/}
227 }</citation> 240 }</citation>
228 </citations> 241 </citations>
229 </tool> 242 </tool>