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comparison gene_family_aligner.xml @ 0:6accbd3a1449 draft

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author greg
date Fri, 07 Apr 2017 13:00:29 -0400
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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>