Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 0:30c4554064f9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Sat, 24 Dec 2016 10:42:48 -0500
parents
children b1e7de636060
comparison
equal deleted inserted replaced
-1:000000000000 0:30c4554064f9
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>