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1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.0">
2 <description>aligns integrated orthologous gene family clusters</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements_gene_family_aligner" />
7 <command detect_errors="exit_code"><![CDATA[
8 #set input_format = $input_format_cond.input_format
9 #set alignment_method_cond = $input_format_cond.alignment_method_cond
10 #set alignment_method = $alignment_method_cond.alignment_method
11 #if str($input_format_cond.input_format) == 'ptortho':
12 #set output_codon_alignments = False
13 #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
14 #set output_codon_alignments = False
15 #else:
16 #set output_codon_alignments = True
17 #end if
18
19 python $__tool_directory__/gene_family_aligner.py
20 --alignment_method $alignment_method
21 #if str($alignment_method) == 'pasta':
22 --pasta_script_path '$__tool_directory__/run_pasta.py'
23 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
24 #end if
25 --num_threads \${GALAXY_SLOTS:-4}
26 #if str($input_format) == 'ptortho':
27 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
28 #else:
29 ## str($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 #end if
34 #end if
35 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
36 #if str($remove_gappy_sequences) == 'yes':
37 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
38 #set trim_type = $trim_type_cond.trim_type
39 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming):
40 --gap_trimming $trim_type_cond.gap_trimming
41 #else:
42 ## str($trim_type) == 'automated_trimming'
43 --automated_trimming 'true'
44 #end if
45 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
46 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
47 #if str($remove_sequences_with_gaps) == 'yes':
48 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of):
49 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
50 #end if
51 #if str($remove_sequences_with_gaps_cond.iterative_realignment):
52 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
53 #end if
54 #if $output_codon_alignments:
55 --output '$output_aln_filtered_ca'
56 --output_dir '$output_aln_filtered_ca.files_path'
57 #else:
58 --output '$output_aln_filtered'
59 --output_dir '$output_aln_filtered.files_path'
60 #end if
61 #else:
62 #if $output_codon_alignments:
63 --output '$output_aln_trimmed_ca'
64 --output_dir '$output_aln_trimmed_ca.files_path'
65 #else:
66 --output '$output_aln_trimmed'
67 --output_dir '$output_aln_trimmed.files_path'
68 #end if
69 #end if
70 #else:
71 #if $output_codon_alignments:
72 --output '$output_aln_ca'
73 --output_dir '$output_aln_ca.files_path'
74 #else:
75 --output '$output_aln'
76 --output_dir '$output_aln.files_path'
77 #end if
78 #end if
79 ]]></command>
80 <inputs>
81 <conditional name="input_format_cond">
82 <param name="input_format" type="select" label="Classified orthogroup fasta files">
83 <option value="ptortho">Proteins orthogroup fasta files</option>
84 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>
85 </param>
86 <when value="ptortho">
87 <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files">
88 <validator type="empty_extra_files_path" />
89 </param>
90 <expand macro="cond_alignment_method" />
91 </when>
92 <when value="ptorthocs">
93 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files">
94 <validator type="empty_extra_files_path" />
95 </param>
96 <expand macro="cond_alignment_method" />
97 <expand macro="param_codon_alignments" />
98 </when>
99 </conditional>
100 <expand macro="cond_remove_gappy_sequences" />
101 </inputs>
102 <outputs>
103 <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}">
104 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
105 </data>
106 <data name="output_aln_ca" format="ptalignca" label="${tool.name} (protein and coding sequences orthogroup alignments) on ${on_string}">
107 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
108 </data>
109 <data name="output_aln_filtered" format="ptalignfiltered" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}">
110 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
111 </data>
112 <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="${tool.name} (filtered protein and coding sequences orthogroup alignments) on ${on_string}">
113 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
114 </data>
115 <data name="output_aln_trimmed" format="ptaligntrimmed" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}">
116 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
117 </data>
118 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}">
119 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
120 </data>
121 </outputs>
122 <tests>
123 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
124 <test>
125 </test>
126 -->
127 </tests>
128 <help>
129 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
130 analyses of genome-scale gene families and transcriptomes. This tool estimates protein and codon multiple sequence alignments
131 of integrated orthologous gene family fasta files produced by the GeneFamilyIntegrator tool.
132
133 -----
134
135 **Required options**
136
137 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
138
139 * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments. PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments.
140
141 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
142
143 * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments. This option requires protein and their corresponding coding sequences to be provided as input data.
144
145 **Other options**
146
147 * **Alignment post-processing configuration** - select 'Yes' to enable multiple sequence alignment post-processing configuration options.
148
149 - **Trimming method** - multiple sequence alignment trimming method. PlantTribes trims alignments using two automated approaches implemented in trimAl. Gap score based trimming removes alignments sites that do not achieve a user specified gap score. For example, a setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. The automated heuristic trimming approach determines the best automated trimAl method to trim a given alignment as described in the trimAl tutorial `trimAl`_.
150
151 - **Gap score** - the fraction of sequences with gap allowed in an alignment site. The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
152
153 - **Remove sequences** - select 'Yes' to remove sequences in multiple sequence alignments that do not achieve a user specified alignment coverage score. For example, a setting of 0.7 removes sequences with more than 30% gaps in the alignment. This option requires one of the trimming methods to be set.
154
155 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
156
157 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect.
158
159 .. _trimAl: http://trimal.cgenomics.org
160
161 </help>
162 <citations>
163 <expand macro="citation1" />
164 <citation type="bibtex">
165 @article{Wall2008,
166 journal = {Nucleic Acids Research},
167 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
168 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
169 year = {2008},
170 volume = {36},
171 number = {suppl 1},
172 pages = {D970-D976},}
173 </citation>
174 <citation type="bibtex">
175 @article{Katoh2013,
176 journal = {Molecular biology and evolution},
177 author = {3. Katoh K, Standley DM},
178 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
179 year = {2013},
180 volume = {30},
181 number = {4},
182 pages = {772-780},}
183 </citation>
184 <citation type="bibtex">
185 @article{Mirarab2014,
186 journal = {Research in Computational Molecular Biology (RECOMB)},
187 author = {4. Mirarab S, Nguyen N, Warnow T},
188 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
189 year = {2014},
190 pages = {177–191},
191 url = {https://github.com/smirarab/pasta},}
192 </citation>
193 <citation type="bibtex">
194 @article{Capella-Gutierrez2009,
195 journal = {Bioinformatics,},
196 author = {5. Capella-Gutierrez S, Silla-Martínez JM, Gabaldón T},
197 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
198 year = {2009},
199 volume = {25},
200 number = {15},
201 pages = {1972-1973},}
202 </citation>
203 </citations>
204 </tool>