|
0
|
1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="0.8.0">
|
|
|
2 <description>aligns gene family sequences</description>
|
|
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements_gene_family_aligner" />
|
|
|
7 <expand macro="stdio" />
|
|
|
8 <command>
|
|
|
9 <![CDATA[
|
|
|
10 #set input_format = $input_format_cond.input_format
|
|
|
11 #set scaffold = $input_format_cond.scaffold
|
|
|
12 #set alignment_method_cond = $input_format_cond.alignment_method_cond
|
|
|
13 #set alignment_method = $alignment_method_cond.alignment_method
|
|
|
14
|
|
|
15 python $__tool_directory__/gene_family_aligner.py
|
|
|
16 --scaffold '$scaffold.fields.path'
|
|
|
17 --method $input_format_cond.method
|
|
|
18 --alignment_method $alignment_method
|
|
|
19 #if str($alignment_method) == 'pasta':
|
|
|
20 --pasta_script_path '$__tool_directory__/run_pasta.py'
|
|
|
21 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
|
|
|
22 #end if
|
|
|
23 --num_threads \${GALAXY_SLOTS:-4}
|
|
|
24 #if str($input_format) == 'ptortho':
|
|
|
25 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
|
|
|
26 --output '$output_ptortho'
|
|
|
27 --output_dir '$output_ptortho.files_path'
|
|
|
28 #else:
|
|
|
29 ## str($input_format) == 'ptorthocs'
|
|
|
30 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
|
|
|
31 #if str($input_format_cond.codon_alignments) == 'yes':
|
|
|
32 --codon_alignments 'true'
|
|
|
33 --output '$output_ptorthocs'
|
|
|
34 --output_dir '$output_ptorthocs.files_path'
|
|
|
35 #else:
|
|
|
36 --output '$output_ptortho'
|
|
|
37 --output_dir '$output_ptortho.files_path'
|
|
|
38 #end if
|
|
|
39 #end if
|
|
|
40 #if str($options_type_cond.options_type) == 'advanced':
|
|
|
41 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
|
|
|
42 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
|
|
|
43 #if str($remove_gappy_sequences) == 'yes':
|
|
|
44 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
|
|
|
45 #set trim_type = $trim_type_cond.trim_type
|
|
|
46 #if str($trim_type) == 'gap_trimming':
|
|
|
47 --gap_trimming $trim_type_cond.gap_trimming
|
|
|
48 #else:
|
|
|
49 ## str($trim_type) == 'automated_trimming'
|
|
|
50 --automated_trimming 'true'
|
|
|
51 #end if
|
|
|
52 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
|
|
|
53 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
|
|
|
54 #if str($remove_sequences_with_gaps) == 'yes':
|
|
|
55 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
|
|
|
56 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
|
|
|
57 #end if
|
|
|
58 #end if
|
|
|
59 #end if
|
|
|
60 ]]>
|
|
|
61 </command>
|
|
|
62 <inputs>
|
|
|
63 <conditional name="input_format_cond">
|
|
|
64 <param name="input_format" type="select" label="Select type of data to sub sample">
|
|
|
65 <option value="ptortho">Gene family clusters</option>
|
|
|
66 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option>
|
|
|
67 </param>
|
|
|
68 <when value="ptortho">
|
|
|
69 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" />
|
|
|
70 <expand macro="param_scaffold" />
|
|
|
71 <expand macro="param_method" />
|
|
|
72 <expand macro="cond_alignment_method" />
|
|
|
73 </when>
|
|
|
74 <when value="ptorthocs">
|
|
|
75 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" />
|
|
|
76 <expand macro="param_scaffold" />
|
|
|
77 <expand macro="param_method" />
|
|
|
78 <expand macro="cond_alignment_method" />
|
|
|
79 <expand macro="param_codon_alignments" />
|
|
|
80 </when>
|
|
|
81 </conditional>
|
|
|
82 <conditional name="options_type_cond">
|
|
|
83 <expand macro="param_options_type" />
|
|
|
84 <when value="basic" />
|
|
|
85 <when value="advanced">
|
|
|
86 <expand macro="cond_remove_gappy_sequences" />
|
|
|
87 </when>
|
|
|
88 </conditional>
|
|
|
89 </inputs>
|
|
|
90 <outputs>
|
|
|
91 <data name="output_ptortho" format="ptortho" label="Integrated gene family clusters on ${on_string}">
|
|
|
92 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter>
|
|
|
93 </data>
|
|
|
94 <data name="output_ptorthocs" format="ptorthocs" label="Integrated gene family clusters and corresponding coding sequences on ${on_string}">
|
|
|
95 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
|
|
|
96 </data>
|
|
|
97 </outputs>
|
|
|
98 <tests>
|
|
|
99 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
|
|
|
100 <test>
|
|
|
101 </test>
|
|
|
102 -->
|
|
|
103 </tests>
|
|
|
104 <help>
|
|
|
105 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
|
|
|
106 analyses of genome-scale gene families and transcriptomes. This tool aligns gene family sequences.
|
|
|
107
|
|
|
108 -----
|
|
|
109
|
|
|
110 **Required options**
|
|
|
111
|
|
|
112 * **Select type of data to sub sample**
|
|
|
113
|
|
|
114 - **Gene family clusters** - sequences classified into gene family clusters.
|
|
|
115 - **Gene family clusters with corresponding coding sequences** - sequences classified into gene family clusters including corresponding coding sequences.
|
|
|
116
|
|
|
117 - **Construct orthogroup multiple codon alignments** - construct orthogroup multiple codon alignments.
|
|
|
118
|
|
|
119 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds [2-4] installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
|
|
|
120 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
|
|
|
121
|
|
|
122 * **Select method for multiple sequence alignments**
|
|
|
123
|
|
|
124 - **MAFFT algorithm** - mafft algorithm.
|
|
|
125 - **Pasta algorithm** - pasta algorithm.
|
|
|
126
|
|
|
127 - **Maximum number of iterations that the PASTA algorithm will execute** - maximum number of iterations that the PASTA algorithm will execute.
|
|
|
128
|
|
|
129 **Other options**
|
|
|
130
|
|
|
131 * **Remove gappy sequences in alignments**
|
|
|
132
|
|
|
133 - **Select process used for gap trimming** - either nucleotide based or using trimAl's ML heuristic trimming approach
|
|
|
134
|
|
|
135 - **Nucleotide based**
|
|
|
136
|
|
|
137 - **Remove sites in alignments with gaps of**
|
|
|
138 - **Maximum number of iterations** - maximum number of iterations for iterative orthogroups realignment, trimming and fitering
|
|
|
139
|
|
|
140 </help>
|
|
|
141 <citations>
|
|
|
142 <expand macro="citation1" />
|
|
|
143 <expand macro="citations2to4" />
|
|
|
144 </citations>
|
|
|
145 </tool>
|
