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comparison phylogenomics_analysis.xml @ 65:534604580eb5 draft

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author greg
date Tue, 28 Feb 2017 09:40:01 -0500
parents c2d2ca6cf94b
children 6d93b214ec55
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64:a0c347192b08 65:534604580eb5
1 <tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.3"> 1 <tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.6.0">
2 <description>and inferred maximum likelihood phylogenies</description> 2 <description>and inferred maximum likelihood phylogenies</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.3">plant_tribes_phylogenomics_analysis 4 <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
5 </requirement>
6 </requirements> 5 </requirements>
7 <stdio> 6 <stdio>
8 <!-- Anything other than zero is an error --> 7 <!-- Anything other than zero is an error -->
9 <exit_code range="1:" /> 8 <exit_code range="1:" />
10 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
16 <![CDATA[ 15 <![CDATA[
17 #import os 16 #import os
18 #import sys 17 #import sys
19 18
20 #set input_format = $input_format_cond.input_format 19 #set input_format = $input_format_cond.input_format
21 #set pipeline_output_dir = 'phylogenomicsAnalysis_dir' 20 #if str($input_format) == 'ptorthocs':
22 #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln')
23 #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta')
24 #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree')
25
26 #if str($input_format) == 'ptortho':
27 #set dest_fasta_dir = $output_fasta_ptortho.extra_files_path
28 #set multiple_codon_alignments = 'no'
29 #set use_corresponding_coding_sequences = 'no'
30 #else:
31 #set dest_fasta_dir = $output_fasta_ptorthocs.extra_files_path
32 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond 21 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
33 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments 22 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
34 #if str($multiple_codon_alignments) == 'yes': 23 #if str($multiple_codon_alignments) == 'yes':
35 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond 24 --sequence_type $multiple_codon_alignments_cond.sequence_type
36 #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences 25 #end if
37 #else: 26 #end if
38 #set use_corresponding_coding_sequences = 'no'
39 #end if
40 #end if
41 mkdir -p $dest_fasta_dir &&
42 27
43 #if str($options_type.options_type_selector) == 'advanced': 28 #if str($options_type.options_type_selector) == 'advanced':
44 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond 29 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
45 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments 30 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
46 #if str($multiple_sequence_alignments) == 'yes': 31 #if str($multiple_sequence_alignments) == 'yes':
47 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 32 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
48 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option 33 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
49 #set generate_output_aln = True 34 #set generate_output_aln = True
50 #set dest_aln_dir = $output_aln.extra_files_path
51 mkdir -p $dest_aln_dir &&
52 #else: 35 #else:
53 #set generate_output_aln = False 36 #set generate_output_aln = False
54 #end if 37 #end if
55 #else: 38 #else:
56 #set generate_output_aln = False 39 #set generate_output_aln = False
57 #end if 40 #end if
58 41
59 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes': 42 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
60 #set generate_output_tree = True 43 #set generate_output_tree = True
61 #set dest_tree_dir = $output_tree.extra_files_path
62 mkdir -p $dest_tree_dir &&
63 #else: 44 #else:
64 #set generate_output_tree = False 45 #set generate_output_tree = False
65 #end if 46 #end if
66 47
67 PhylogenomicsAnalysis 48 python $__tool_directory__/phylogenomics_analysis.py
68 --num_threads \${GALAXY_SLOTS:-4} 49 --num_threads \${GALAXY_SLOTS:-4}
69 #if str($input_format) == 'ptortho': 50 #if str($input_format) == 'ptortho':
70 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 51 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
71 #else: 52 #else:
72 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 53 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
73 --orthogroup_fna 54 --orthogroup_fna 'true'
74 #end if 55 #end if
75 --config_dir '$scaffold.fields.path' 56 --config_dir '$scaffold.fields.path'
76 --scaffold '$scaffold.fields.path' 57 --scaffold '$scaffold.fields.path'
77 --method $method 58 --method $method
78 59
79 #if str($options_type.options_type_selector) == 'advanced': 60 #if str($options_type.options_type_selector) == 'advanced':
80 #if str($multiple_sequence_alignments) == 'yes': 61 #if str($multiple_sequence_alignments) == 'yes':
81 #if str($multiple_sequence_alignments_option) == 'create_alignments': 62 --alignments_method $multiple_sequence_alignments_option
82 --create_alignments 63 if str($multiple_sequence_alignments_option) == 'pasta_alignments':
83 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
84 --add_alignments
85 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
86 --pasta_script_path '$__tool_directory__/run_pasta.py' 64 --pasta_script_path '$__tool_directory__/run_pasta.py'
87 --pasta_alignments
88 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit 65 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
89 #end if 66 #end if
90 #end if 67 #end if
91 68
92 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes': 69 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
96 #if str($tree_inference_method) == 'raxml': 73 #if str($tree_inference_method) == 'raxml':
97 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 74 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
98 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 75 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
99 #if str($rooting_order_file) == 'yes': 76 #if str($rooting_order_file) == 'yes':
100 --rooting_order '$rooting_order_file_cond.rooting_order' 77 --rooting_order '$rooting_order_file_cond.rooting_order'
101 # No else block needed here because the default rooting_order 78 # No else block needed here because the default rooting_order
102 # configuration will be used if the --rooting_order flag is missing. 79 # configuration will be used if the --rooting_order flag is missing.
103 #end if 80 #end if
104 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates 81 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
105 #end if 82 #end if
106 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size 83 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
107 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size 84 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size
111 #set msa_quality_control_options_cond = $options_type.msa_quality_control_options_cond 88 #set msa_quality_control_options_cond = $options_type.msa_quality_control_options_cond
112 #set remove_gappy_sequences_cond = $msa_quality_control_options_cond.remove_gappy_sequences_cond 89 #set remove_gappy_sequences_cond = $msa_quality_control_options_cond.remove_gappy_sequences_cond
113 #if str($remove_gappy_sequences_cond) == 'yes': 90 #if str($remove_gappy_sequences_cond) == 'yes':
114 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 91 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
115 --remove_sequences $remove_gappy_sequences_cond.remove_sequences 92 --remove_sequences $remove_gappy_sequences_cond.remove_sequences
116 #if str($trim_type_cond.trim_type) == 'automated_trimming': 93 --trim_type $trim_type_cond.trim_type
117 --automated_trimming 94 #if str($trim_type_cond.trim_type) == 'gap_trimming':
118 #else:
119 --gap_trimming $trim_type_cond.gap_trimming 95 --gap_trimming $trim_type_cond.gap_trimming
120 #end if 96 #end if
121 #end if 97 #end if
122 #end if 98 #end if
123 #end if 99 #end if
124 >/dev/null 100
125
126 && echo "Sequence alignments and corresponding phylogenies"
127 #if str($input_format) == 'ptortho': 101 #if str($input_format) == 'ptortho':
128 && echo -e "#Size\tName" > $output_fasta_ptortho 102 --output_ptortho '$output_ptortho'
129 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho 103 --output_ptortho_dir '$output_ptortho.files_path'
130 #else: 104 #else:
131 && echo -e "#Size\tName" > $output_fasta_ptorthocs 105 --output_ptorthocs '$output_ptorthocs'
132 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs 106 --output_ptorthocs_dir '$output_ptorthocs.files_path'
133 #end if 107 #end if
134 && mv $src_fasta_dir/* $dest_fasta_dir || true
135 108
136 #if $generate_output_aln: 109 #if $generate_output_aln:
137 && echo -e "#Size\tName" > $output_aln 110 --output_aln '$output_aln'
138 && ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln 111 --output_aln_dir '$output_aln.files_path'
139 && mv $src_aln_dir/* $dest_aln_dir || true
140 #end if 112 #end if
141 113
142 #if $generate_output_tree: 114 #if $generate_output_tree:
143 && echo -e "#Size\tName" > $output_tree 115 --output_tree '$output_tree'
144 && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree 116 --output_tree_dir '$output_tree.files_path'
145 && mv $src_tree_dir/* $dest_tree_dir || true
146 #end if 117 #end if
147 ]]> 118 ]]>
148 </command> 119 </command>
149 <inputs> 120 <inputs>
150 <conditional name="input_format_cond"> 121 <conditional name="input_format_cond">
166 <when value="yes"> 137 <when value="yes">
167 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)"> 138 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
168 <option value="protein" selected="true">Amino acid based</option> 139 <option value="protein" selected="true">Amino acid based</option>
169 <option value="dna">Nucleotide based</option> 140 <option value="dna">Nucleotide based</option>
170 </param> 141 </param>
171 <conditional name="use_corresponding_coding_sequences_cond">
172 <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences?">
173 <option value="no" selected="true">No</option>
174 <option value="yes">Yes</option>
175 </param>
176 <when value="no" />
177 <when value="yes" />
178 </conditional>
179 </when> 142 </when>
180 </conditional> 143 </conditional>
181 </when> 144 </when>
182 </conditional> 145 </conditional>
183 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 146 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
211 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option> 174 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
212 </param> 175 </param>
213 <when value="create_alignments" /> 176 <when value="create_alignments" />
214 <when value="add_alignments" /> 177 <when value="add_alignments" />
215 <when value="pasta_alignments"> 178 <when value="pasta_alignments">
216 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will run" /> 179 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will execute" />
217 </when> 180 </when>
218 </conditional> 181 </conditional>
219 </when> 182 </when>
220 </conditional> 183 </conditional>
221 <conditional name="phylogenetic_trees_cond"> 184 <conditional name="phylogenetic_trees_cond">
280 </conditional> 243 </conditional>
281 </when> 244 </when>
282 </conditional> 245 </conditional>
283 </inputs> 246 </inputs>
284 <outputs> 247 <outputs>
285 <data name="output_fasta_ptortho" format="ptortho"> 248 <data name="output_ptortho" format="ptortho">
286 <filter>input_format_cond['input_format'] == 'ptortho'</filter> 249 <filter>input_format_cond['input_format'] == 'ptortho'</filter>
287 </data> 250 </data>
288 <data name="output_fasta_ptorthocs" format="ptorthocs"> 251 <data name="output_ptorthocs" format="ptorthocs">
289 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter> 252 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
290 </data> 253 </data>
291 <data name="output_aln" format="ptalign" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}"> 254 <data name="output_aln" format="ptalign" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}">
292 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter> 255 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
293 </data> 256 </data>