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comparison align_seqs.xml @ 0:31be13116b46 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:15:56 -0400
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-1:000000000000 0:31be13116b46
1 <tool id="qiime_align_seqs" name="Align sequences" version="@WRAPPER_VERSION@.0">
2 <description>using a variety of alignment methods</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="1.0.2">infernal</requirement>
8 <requirement type="package" version="2.1">clustalw</requirement>
9 <requirement type="package" version="3.8.1551">muscle</requirement>
10 <requirement type="package" version="7.305">mafft</requirement>
11 <requirement type="package" version="2.2.22">blast-legacy</requirement>
12 </expand>
13 <version_command>align_seqs.py --version</version_command>
14 <command detect_errors="aggressive"><![CDATA[
15 align_seqs.py
16 --input_fasta_fp '$input_fasta_fp'
17 -o output
18 --alignment_method '$alignment.alignment_method'
19 #if $alignment.alignment_method == 'pynast'
20 --pairwise_alignment_method '$alignment.pairwise_alignment_method'
21 #if str($alignment.template_fp) != 'None':
22 --template_fp '$alignment.template_fp'
23 #end if
24 #elif $alignment.alignment_method == 'infernal'
25 --template_fp '$alignment.template_fp'
26 #end if
27
28 #if $min_length:
29 --min_length '$min_length'
30 #end if
31 --min_percent_id '$min_percent_id'
32 ]]></command>
33 <inputs>
34 <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/>
35 <conditional name="alignment">
36 <param argument="--alignment_method" type="select" label="Method for aligning sequences">
37 <option value="pynast" selected="True">pynast</option>
38 <option value="infernal">infernal</option>
39 <option value="clustalw">clustalw</option>
40 <option value="muscle">muscle</option>
41 <option value="mafft">mafft</option>
42 </param>
43 <when value="pynast">
44 <param argument="--pairwise_alignment_method" type="select" label="Method for performing pairwise alignment in PyNAST">
45 <option value="muscle">muscle</option>
46 <option value="pair_hmm">pair_hmm</option>
47 <option value="clustal">clustal</option>
48 <option value="blast">blast</option>
49 <option value="uclust" selected="True">uclust</option>
50 <option value="mafft">mafft</option>
51 </param>
52 <param argument="--template_fp" type="data" format="fasta" optional="True" label="Fasta file for template alignment"/>
53 </when>
54 <when value="infernal">
55 <param argument="--template_fp" type="data" format="stockholm" label="Stockholm file with a corresponding secondary structure annotation"/>
56 </when>
57 <when value="clustalw"/>
58 <when value="muscle"/>
59 <when value="mafft"/>
60 </conditional>
61 <param argument="--min_length" type="integer" optional="True" label="Minimum sequence length to include in alignment" help="By default, 75% of the median input sequence length"/>
62 <param argument="--min_percent_id" type="float" value="0.75" label="Minimum percent sequence identity to closest blast hit to include sequence in alignment"/>
63 </inputs>
64 <outputs>
65 <data name="aligned_sequences" format="fasta" from_work_dir="output/*_aligned.fasta" label="${tool.name} on ${on_string}: Aligned sequences"/>
66 <data name="failures_sequences" format="fasta" from_work_dir="output/*_failures.fasta" label="${tool.name} on ${on_string}: Failure sequences">
67 <filter>alignment['alignment_method'] == 'pynast'</filter>
68 </data>
69 <data name="log" format="txt" from_work_dir="output/*_log.txt" label="${tool.name} on ${on_string}: Log"/>
70 </outputs>
71 <tests>
72 <test><!-- 1 -->
73 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
74 <param name="alignment_method" value="pynast"/>
75 <param name="pairwise_alignment_method" value="uclust" />
76 <param name="min_percent_id" value="0.75"/>
77 <param name="template_fp" value="align_seqs/core_set_aligned.fasta.imputed"/>
78 <output name="aligned_sequences">
79 <assert_contents>
80 <has_text text="r0 PC.634_176 RC:1..246"/>
81 <has_text text="r102 PC.634_91 RC:1..238"/>
82 <has_text text="New.0.CleanUp.ReferenceOTU9 PC.355_327 RC:1..244"/>
83 </assert_contents>
84 </output>
85 <output name="failures_sequences">
86 <assert_contents>
87 <has_text text="r111 PC.634_173"/>
88 <has_text text="New.0.ReferenceOTU52 PC.636_379"/>
89 <has_text text="New.0.CleanUp.ReferenceOTU33 PC.607_365"/>
90 </assert_contents>
91 </output>
92 <output name="log">
93 <assert_contents>
94 <has_text text="PC.634_176"/>
95 <has_text text="New.0.ReferenceOTU13"/>
96 <has_text text="min_len:176"/>
97 </assert_contents>
98 </output>
99 </test>
100 <test><!-- 2 -->
101 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
102 <param name="alignment_method" value="pynast"/>
103 <param name="pairwise_alignment_method" value="muscle" />
104 <param name="min_length" value="50" />
105 <param name="min_percent_id" value="0.75" />
106 <output name="aligned_sequences">
107 <assert_contents>
108 <has_text text="r0 PC.634_176 RC:1..246"/>
109 <has_text text="r102 PC.634_91 RC:1..238"/>
110 <has_text text="New.0.CleanUp.ReferenceOTU9 PC.355_327 RC:1..244"/>
111 </assert_contents>
112 </output>
113 <output name="failures_sequences" md5="d41d8cd98f00b204e9800998ecf8427e"/>
114 <output name="log">
115 <assert_contents>
116 <has_text text="PC.634_176"/>
117 <has_text text="New.0.ReferenceOTU13"/>
118 <has_text text="min_len:50"/>
119 </assert_contents>
120 </output>
121 </test>
122 <test><!-- 3 -->
123 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
124 <param name="alignment_method" value="pynast"/>
125 <param name="pairwise_alignment_method" value="pair_hmm" />
126 <param name="min_percent_id" value="0.75" />
127 <output name="aligned_sequences">
128 <assert_contents>
129 <has_text text="r0 PC.634_176 RC:1..246"/>
130 <has_text text="r102 PC.634_91 RC:1..238"/>
131 <has_text text="New.0.CleanUp.ReferenceOTU9 PC.355_327 RC:1..244"/>
132 </assert_contents>
133 </output>
134 <output name="failures_sequences" md5="d41d8cd98f00b204e9800998ecf8427e"/>
135 <output name="log">
136 <assert_contents>
137 <has_text text="PC.634_176"/>
138 <has_text text="New.0.ReferenceOTU13"/>
139 <has_text text="min_len:176"/>
140 </assert_contents>
141 </output>
142 </test>
143 <test><!-- 4 -->
144 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
145 <param name="alignment_method" value="pynast"/>
146 <param name="pairwise_alignment_method" value="clustal" />
147 <param name="min_percent_id" value="0.75" />
148 <output name="aligned_sequences">
149 <assert_contents>
150 <has_text text="PC.634_176"/>
151 <has_text text="ReferenceOTU7"/>
152 </assert_contents>
153 </output>
154 <output name="failures_sequences" md5="d41d8cd98f00b204e9800998ecf8427e"/>
155 <output name="log">
156 <assert_contents>
157 <has_text text="PC.634_176"/>
158 <has_text text="ReferenceOTU7"/>
159 </assert_contents>
160 </output>
161 </test>
162 <test><!-- 5 -->
163 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
164 <param name="alignment_method" value="pynast"/>
165 <param name="pairwise_alignment_method" value="blast" />
166 <param name="min_percent_id" value="0.75" />
167 <output name="aligned_sequences">
168 <assert_contents>
169 <has_text text="r0 PC.634_176 RC:1..246"/>
170 <has_text text="r102 PC.634_91 RC:1..238"/>
171 <has_text text="New.0.CleanUp.ReferenceOTU9 PC.355_327 RC:1..244"/>
172 </assert_contents>
173 </output>
174 <output name="failures_sequences" md5="d41d8cd98f00b204e9800998ecf8427e"/>
175 <output name="log">
176 <assert_contents>
177 <has_text text="PC.634_176"/>
178 <has_text text="New.0.ReferenceOTU13"/>
179 <has_text text="min_len:176"/>
180 </assert_contents>
181 </output>
182 </test>
183 <test><!-- 6 -->
184 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
185 <param name="alignment_method" value="pynast"/>
186 <param name="pairwise_alignment_method" value="mafft" />
187 <param name="min_percent_id" value="0.75" />
188 <output name="aligned_sequences">
189 <assert_contents>
190 <has_text text="r0 PC.634_176 RC:1..246"/>
191 <has_text text="r102 PC.634_91 RC:1..238"/>
192 <has_text text="New.0.CleanUp.ReferenceOTU9 PC.355_327 RC:1..244"/>
193 </assert_contents>
194 </output>
195 <output name="failures_sequences" md5="d41d8cd98f00b204e9800998ecf8427e"/>
196 <output name="log">
197 <assert_contents>
198 <has_text text="PC.634_176"/>
199 <has_text text="New.0.ReferenceOTU13"/>
200 <has_text text="min_len:176"/>
201 </assert_contents>
202 </output>
203 </test>
204 <!-- TODO: fix infernal test -->
205 <!--<test><!- - 7 - ->
206 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
207 <param name="alignment_method" value="infernal"/>
208 <param name="template_fp" value="align_seqs/core_set_aligned.fasta.imputed"/>
209 <output name="aligned_sequences">
210 <assert_contents>
211 <has_text text="PC.356_295"/>
212 <has_text text="ReferenceOTU28"/>
213 </assert_contents>
214 </output>
215 <output name="log">
216 <assert_contents>
217 <has_text text="PC.356_295"/>
218 <has_text text="ReferenceOTU28"/>
219 </assert_contents>
220 </output>
221 </test>-->
222 <test><!-- 8 -->
223 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
224 <param name="alignment_method" value="clustalw"/>
225 <param name="min_percent_id" value="0.75" />
226 <output name="aligned_sequences">
227 <assert_contents>
228 <has_text text="PC.356_295"/>
229 <has_text text="ReferenceOTU28"/>
230 </assert_contents>
231 </output>
232 <output name="log">
233 <assert_contents>
234 <has_text text="CogentAligner"/>
235 </assert_contents>
236 </output>
237 </test>
238 <test><!-- 9 -->
239 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
240 <param name="alignment_method" value="muscle"/>
241 <param name="min_percent_id" value="0.75" />
242 <output name="aligned_sequences">
243 <assert_contents>
244 <has_text text="r143 PC.356_295"/>
245 <has_text text="r70 PC.593_22"/>
246 <has_text text="r178 PC.634_139"/>
247 </assert_contents>
248 </output>
249 <output name="log">
250 <assert_contents>
251 <has_text text="CogentAligner parameters"/>
252 <has_text text="Method:muscle"/>
253 </assert_contents>
254 </output>
255 </test>
256 <test><!-- 10 -->
257 <param name="input_fasta_fp" value="align_seqs/unaligned.fna"/>
258 <param name="alignment_method" value="mafft"/>
259 <param name="min_percent_id" value="0.75" />
260 <output name="aligned_sequences">
261 <assert_contents>
262 <has_text text="r143 PC.356_295"/>
263 <has_text text="r175 PC.634_133"/>
264 <has_text text="r178 PC.634_139"/>
265 </assert_contents>
266 </output>
267 <output name="log">
268 <assert_contents>
269 <has_text text="CogentAligner parameters"/>
270 <has_text text="Method:mafft"/>
271 </assert_contents>
272 </output>
273 </test>
274 </tests>
275 <help><![CDATA[
276 **What it does**
277
278 This tool aligns the sequences in a FASTA file to each other or to a template sequence alignment, depending on the method chosen.
279
280 More information about this tool is available on
281 `QIIME documentation <http://qiime.org/scripts/align_seqs.html>`_.
282 ]]></help>
283 <citations>
284 <expand macro="citations"/>
285 <citation type="doi">10.1093/bioinformatics/btp636</citation>
286 <citation type="doi">10.1093/nar/gkh340</citation>
287 <citation type="doi">10.1093/bioinformatics/btp157</citation>
288 </citations>
289 </tool>