|
0
|
1 <tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="1.0.0">
|
|
|
2 <description>pipeline</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="0.2">plant_tribes_phylogenomics_analysis</requirement>
|
|
|
5 </requirements>
|
|
|
6 <stdio>
|
|
|
7 <!-- Anything other than zero is an error -->
|
|
|
8 <exit_code range="1:" />
|
|
|
9 <!-- In case the return code has not been set properly check stderr too -->
|
|
|
10 <regex match="Error:" />
|
|
|
11 <regex match="Exception:" />
|
|
|
12 </stdio>
|
|
|
13 <command>
|
|
|
14 <![CDATA[
|
|
|
15 PhylogenomicsAnalysis
|
|
|
16 ----orthogroup_faa "$orthogroup_fna.extra_files_path"
|
|
|
17 --scaffold "$scaffold"
|
|
|
18 --method $method
|
|
|
19 #if str($options_type.options_type_selector) == 'advanced':
|
|
|
20 #if str($options_type.multiple_sequence_alignments_cond) == 'yes':
|
|
|
21 #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
|
|
|
22 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
|
|
|
23 #if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'create_alignments':
|
|
|
24 --create_alignments
|
|
|
25 #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'add_alignments':
|
|
|
26 --add_alignments
|
|
|
27 #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'pasta_alignments':
|
|
|
28 --pasta_alignments
|
|
|
29 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
|
|
|
30 #end if
|
|
|
31 #if str($multiple_codon_alignments_cond.multiple_codon_alignments) == 'yes':
|
|
|
32 --codon_alignments
|
|
|
33 --orthogroup_fna "$orthogroup_fna"
|
|
|
34 --sequence_type $multiple_codon_alignments_cond.sequence_type
|
|
|
35 #end if
|
|
|
36 #end if
|
|
|
37 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
|
|
|
38 #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond
|
|
|
39 #set tree_inference_method = $tree_inference_cond.tree_inference
|
|
|
40 --tree_inference $tree_inference_method
|
|
|
41 #if str($tree_inference_method) == 'raxml':
|
|
|
42 --rooting_order "$tree_inference_cond.rooting_order"
|
|
|
43 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
|
|
|
44 #end if
|
|
|
45 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
|
|
|
46 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size
|
|
|
47 #end if
|
|
|
48 #if str($options_type.msa_quality_control_options_cond.msa_quality_control_options) == 'yes':
|
|
|
49 #set msa_quality_control_options_cond = $options_type.msa_quality_control_options_cond
|
|
|
50 #set remove_gappy_sequences_cond = $msa_quality_control_options_cond.remove_gappy_sequences_cond
|
|
|
51 #if str($remove_gappy_sequences_cond) == 'yes':
|
|
|
52 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
|
|
|
53 --remove_sequences $remove_gappy_sequences_cond.remove_sequences
|
|
|
54 #if str($trim_type_cond.trim_type) == 'automated_trimming':
|
|
|
55 --automated_trimming
|
|
|
56 else:
|
|
|
57 --gap_trimming $trim_type_cond.gap_trimming
|
|
|
58 #end if
|
|
|
59 #end if
|
|
|
60 #end if
|
|
|
61 #end if
|
|
|
62 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
|
|
|
63 --num_threads \${GALAXY_SLOTS:-4}
|
|
|
64 ]]>
|
|
|
65 </command>
|
|
|
66 <inputs>
|
|
|
67 <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/>
|
|
|
68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
|
|
|
69 <options from_data_table="plant_tribes_scaffolds" />
|
|
|
70 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
|
|
|
71 </param>
|
|
|
72 <param name="method" type="select" label="Protein clustering method">
|
|
|
73 <option value="gfam" selected="true">GFam</option>
|
|
|
74 <option value="orthofinder">OrthoFinder</option>
|
|
|
75 <option value="orthomcl">OrthoMCL</option>
|
|
|
76 </param>
|
|
|
77 <conditional name="options_type">
|
|
|
78 <param name="options_type_selector" type="select" label="Options Configuration">
|
|
|
79 <option value="basic" selected="true">Basic</option>
|
|
|
80 <option value="advanced">Advanced</option>
|
|
|
81 </param>
|
|
|
82 <when value="basic" />
|
|
|
83 <when value="advanced">
|
|
|
84 <conditional name="multiple_sequence_alignments_cond">
|
|
|
85 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignemnts options?">
|
|
|
86 <option value="no" selected="true">No</option>
|
|
|
87 <option value="yes">Yes</option>
|
|
|
88 </param>
|
|
|
89 <when value="no" />
|
|
|
90 <when value="yes">
|
|
|
91 <conditional name="multiple_sequence_alignments_option_cond">
|
|
|
92 <param name="multiple_sequence_alignments_option" label="Select option" type="select" force_select="True">
|
|
|
93 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
|
|
|
94 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
|
|
|
95 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
|
|
|
96 </param>
|
|
|
97 <when value="create_alignments"/>
|
|
|
98 <when value="add_alignments"/>
|
|
|
99 <when value="pasta_alignments">
|
|
|
100 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will run"/>
|
|
|
101 </when>
|
|
|
102 </conditional>
|
|
|
103 <conditional name="multiple_codon_alignments_cond">
|
|
|
104 <param name="multiple_codon_alignments" label="Construct orthogroup multiple codon alignments?" type="select">
|
|
|
105 <option value="no" selected="True">No</option>
|
|
|
106 <option value="yes">Yes</option>
|
|
|
107 </param>
|
|
|
108 <when value="yes">
|
|
|
109 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference - (dna)">
|
|
|
110 <option value="protein" selected="true">Amino acid based</option>
|
|
|
111 <option value="dna">Nucleotide based</option>
|
|
|
112 </param>
|
|
|
113 </when>
|
|
|
114 <when value="no"/>
|
|
|
115 </conditional>
|
|
|
116 </when>
|
|
|
117 </conditional>
|
|
|
118 <conditional name="phylogenetic_trees_cond">
|
|
|
119 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
|
|
|
120 <option value="no" selected="true">No</option>
|
|
|
121 <option value="yes">Yes</option>
|
|
|
122 </param>
|
|
|
123 <when value="no" />
|
|
|
124 <when value="yes">
|
|
|
125 <conditional name="tree_inference_cond">
|
|
|
126 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
|
|
|
127 <option value="raxml" selected="true">RAxML</option>
|
|
|
128 <option value="fasttree">FastTree</option>
|
|
|
129 </param>
|
|
|
130 <when value="raxml">
|
|
|
131 <param name="rooting_order" format="txt" type="data" label="Select file containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees"/>
|
|
|
132 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree"/>
|
|
|
133 </when>
|
|
|
134 <when value="fasttree"/>
|
|
|
135 </conditional>
|
|
|
136 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments"/>
|
|
|
137 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments"/>
|
|
|
138 </when>
|
|
|
139 </conditional>
|
|
|
140 <conditional name="msa_quality_control_options_cond">
|
|
|
141 <param name="msa_quality_control_options" type="select" label="Set MSA quality control options?">
|
|
|
142 <option value="no" selected="true">No</option>
|
|
|
143 <option value="yes">Yes</option>
|
|
|
144 </param>
|
|
|
145 <when value="no" />
|
|
|
146 <when value="yes">
|
|
|
147 <conditional name="remove_gappy_sequences_cond">
|
|
|
148 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
|
|
|
149 <option value="no" selected="true">No</option>
|
|
|
150 <option value="yes">Yes</option>
|
|
|
151 </param>
|
|
|
152 <when value="no"/>
|
|
|
153 <when value="yes">
|
|
|
154 <param name="remove_sequences" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps"/>
|
|
|
155 <conditional name="trim_type_cond">
|
|
|
156 <param name="trim_type" type="select" label="Select process used for gap trimming">
|
|
|
157 <option value="automated_trimming" selected="true">Trim alignments using trimAl's ML heuristic trimming approach</option>
|
|
|
158 <option value="gap_trimming">Nucleotide based</option>
|
|
|
159 </param>
|
|
|
160 <when value="automated_trimming"/>
|
|
|
161 <when value="gap_trimming">
|
|
|
162 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps"/>
|
|
|
163 </when>
|
|
|
164 </conditional>
|
|
|
165 </when>
|
|
|
166 </conditional>
|
|
|
167 </when>
|
|
|
168 </conditional>
|
|
|
169 </when>
|
|
|
170 </conditional>
|
|
|
171 </inputs>
|
|
|
172 <outputs>
|
|
|
173 <collection name="transcripts" type="list">
|
|
|
174 <discover_datasets pattern="__name__" directory="phylogenomicsAnalysis_dir" visible="true" ext="fasta" />
|
|
|
175 </collection>
|
|
|
176 </outputs>
|
|
|
177 <tests>
|
|
|
178 <test>
|
|
|
179 <param name="input" value="" ftype="fasta" />
|
|
|
180 <param name="prediction_method" value="transdecoder"/>
|
|
|
181 <param name="target_gene_family_assembly" value="no"/>
|
|
|
182 <param name="strand_specific" value="yes"/>
|
|
|
183 <param name="dereplicate" value="yes"/>
|
|
|
184 <param name="min_length" value="200"/>
|
|
|
185 <output_collection name="orthos" type="list">
|
|
|
186
|
|
|
187 </output_collection>
|
|
|
188 </test>
|
|
|
189 </tests>
|
|
|
190 <help>
|
|
|
191 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
|
|
|
192 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
|
|
|
193 analyses, comparing and analyzing the sequences of single genes, or a small number of genes, as well as many other types of data.
|
|
|
194
|
|
|
195 -----
|
|
|
196
|
|
|
197 **Options**
|
|
|
198
|
|
|
199 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
|
|
|
200 * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
|
|
|
201 * **Protein classification method** - One of blastp, HMMScan or both.
|
|
|
202 * **SuperOrthogroups MCL clustering** - blastp e-value matrix between all pairs of orthogroups.
|
|
|
203 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
|
|
|
204 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
|
|
|
205 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
|
|
|
206
|
|
|
207 </help>
|
|
|
208 <citations>
|
|
|
209 <citation type="bibtex">
|
|
|
210 @unpublished{None,
|
|
|
211 author = {None},
|
|
|
212 title = {None},
|
|
|
213 year = {None},
|
|
|
214 eprint = {None},
|
|
|
215 url = {None}
|
|
|
216 }</citation>
|
|
|
217 </citations>
|
|
|
218 </tool>
|
