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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:59:28 -0400
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1 <tool id="sniplay_readseq" name="Readseq" version="2.0.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Convert various alignment formats </description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="2.1.30">readseq</requirement>
10 </requirements>
11
12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <stdio>
14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
15 <exit_code range="1:" level="fatal" />
16 </stdio>
17
18 <!-- [REQUIRED] The command to execute -->
19 <command>
20 readseq $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp;
21 #if str( $format ) == "1":
22 mv ${filein}.ig $fileout
23 #elif str( $format ) == "2" :
24 mv ${filein}.gb $fileout
25 #elif str( $format ) == "3" :
26 mv ${filein}.nbrf $fileout
27 #elif str( $format ) == "4" :
28 mv ${filein}.embl $fileout
29 #elif str( $format ) == "5" :
30 mv ${filein}.gcg $fileout
31 #elif str( $format ) == "6" :
32 mv ${filein}.strider $fileout
33 #elif str( $format ) == "8" :
34 mv ${filein}.fasta $fileout
35 #elif str( $format ) == "11" :
36 mv ${filein}.phylip2 $fileout
37 #elif str( $format ) == "12" :
38 mv ${filein}.phylip $fileout
39 #elif str( $format ) == "13" :
40 mv ${filein}.seq $fileout
41 #elif str( $format ) == "14" :
42 mv ${filein}.pir $fileout
43 #elif str( $format ) == "15" :
44 mv ${filein}.msf $fileout
45 #elif str( $format ) == "17" :
46 mv ${filein}.nexus $fileout
47 #elif str( $format ) == "18" :
48 mv ${filein}.pretty $fileout
49 #elif str( $format ) == "19" :
50 mv ${filein}.xml $fileout
51 #elif str( $format ) == "22" :
52 mv ${filein}.aln $fileout
53 #elif str( $format ) == "25" :
54 mv ${filein}.ace $fileout
55 #end if
56 </command>
57
58 <!-- [REQUIRED] Input files and tool parameters -->
59 <inputs>
60 <param name="filein" type="data" format="fasta" optional="false" label="Fasta alignment input" />
61 <param name="fileout_label" type="text" value="phylip conversion" label="Output name" help="Output name for files" />
62 <param name="format" type="select" label="Output format" >
63 <option value="1">1.IG|Stanford</option>
64 <option value="2">2.GenBank|gb</option>
65 <option value="3">3.NBRF</option>
66 <option value="4">4.EMBL|em</option>
67 <option value="5">5.GCG</option>
68 <option value="6">6.DNAStrider</option>
69 <option value="8">8.Pearson|Fasta|fa</option>
70 <option value="11">11.Phylip3.2</option>
71 <option value="12" selected="true">12.Phylip|Phylip4</option>
72 <option value="13">13.Plain|Raw</option>
73 <option value="14">14.PIR|CODATA</option>
74 <option value="15">15.MSF</option>
75 <option value="17">17.PAUP|NEXUS</option>
76 <option value="18">18.Pretty</option>
77 <option value="19">19.XML</option>
78 <option value="22">22.Clustal</option>
79 <option value="25">25.ACEDB</option>
80 </param>
81 </inputs>
82
83 <!-- [REQUIRED] Output files -->
84 <outputs>
85 <data name="fileout_log" format="txt" label="${fileout_label}.log" />
86 <data name="fileout" format="txt" label="${fileout_label}" >
87 <change_format>
88 <when input="format" value="1" format="ig" />
89 <when input="format" value="2" format="genbank" />
90 <when input="format" value="4" format="embl" />
91 <when input="format" value="5" format="gcg" />
92 <when input="format" value="6" format="strider" />
93 <when input="format" value="8" format="fasta" />
94 <when input="format" value="11" format="phylip" />
95 <when input="format" value="12" format="phylip" />
96 <when input="format" value="14" format="pir" />
97 <when input="format" value="17" format="nexus" />
98 <when input="format" value="18" format="prettyseq" />
99 <when input="format" value="19" format="xml" />
100 <when input="format" value="22" format="clustal" />
101 <when input="format" value="25" format="acedb" />
102 </change_format>
103 </data>
104 </outputs>
105
106 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
107 <tests>
108 <!-- [HELP] Test files have to be in the ~/test-data directory -->
109 <test>
110 <param name="filein" value="readseq-alignment.fa" />
111 <param name="format" value="1" />
112 <output name="fileout" file="readseq-standford" />
113 </test>
114 <test>
115 <param name="filein" value="readseq-alignment.fa" />
116 <param name="format" value="2" />
117 <output name="fileout" file="readseq-GenBank" />
118 </test>
119 <test>
120 <param name="filein" value="readseq-alignment.fa" />
121 <param name="format" value="3" />
122 <output name="fileout" file="readseq-NBRF" />
123 </test>
124 <test>
125 <param name="filein" value="readseq-alignment.fa" />
126 <param name="format" value="4" />
127 <output name="fileout" file="readseq-EMBL" />
128 </test>
129 <test>
130 <param name="filein" value="readseq-alignment.fa" />
131 <param name="format" value="5" />
132 <assert_command>
133 <has_text text="-f 5" />
134 <has_text text=".gcg" />
135 </assert_command>
136 </test>
137 <test>
138 <param name="filein" value="readseq-alignment.fa" />
139 <param name="format" value="6" />
140 <output name="fileout" file="readseq-DNAStrider" />
141 </test>
142 <test>
143 <param name="filein" value="readseq-alignment.fa" />
144 <param name="format" value="8" />
145 <output name="fileout" file="readseq-Pearson" />
146 </test>
147 <test>
148 <param name="filein" value="readseq-alignment.fa" />
149 <param name="format" value="11" />
150 <output name="fileout" file="readseq-phylip32" />
151 </test>
152 <test>
153 <param name="filein" value="readseq-alignment.fa" />
154 <param name="format" value="12" />
155 <output name="fileout" file="readseq-phylip" />
156 </test>
157 <test>
158 <param name="filein" value="readseq-alignment.fa" />
159 <param name="format" value="13" />
160 <output name="fileout" file="readseq-raw" />
161 </test>
162 <test>
163 <param name="filein" value="readseq-alignment.fa" />
164 <param name="format" value="14" />
165 <output name="fileout" file="readseq-PIR" />
166 </test>
167 <test>
168 <param name="filein" value="readseq-alignment.fa" />
169 <param name="format" value="15" />
170 <output name="fileout" file="readseq-MSF.txt" lines_diff="2" />
171 </test>
172 <test>
173 <param name="filein" value="readseq-alignment.fa" />
174 <param name="format" value="17" />
175 <output name="fileout" file="readseq-NEXUS" />
176 </test>
177 <test>
178 <param name="filein" value="readseq-alignment.fa" />
179 <param name="format" value="18" />
180 <output name="fileout" file="readseq-Pretty" />
181 </test>
182 <test>
183 <param name="filein" value="readseq-alignment.fa" />
184 <param name="format" value="19" />
185 <output name="fileout" file="readseq-XML" />
186 </test>
187 <test>
188 <param name="filein" value="readseq-alignment.fa" />
189 <param name="format" value="22" />
190 <output name="fileout" file="readseq-Clustal" />
191 </test>
192 <test>
193 <param name="filein" value="readseq-alignment.fa" />
194 <param name="format" value="25" />
195 <output name="fileout" file="readseq-ACEDB" />
196 </test>
197
198 </tests>
199
200 <!-- [OPTIONAL] Help displayed in Galaxy -->
201 <help><![CDATA[
202
203 .. class:: infomark
204
205 **Authors** Don Gilbert software@bio.indiana.edu
206
207 | **Please cite** If you use this tool, please cite Don Gilbert software@bio.indiana.edu
208
209 .. class:: infomark
210
211 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
212
213 .. class:: infomark
214
215 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
216
217 ---------------------------------------------------
218
219 =======
220 Readseq
221 =======
222
223 -----------
224 Description
225 -----------
226
227 | Compute a phylip tree from a fasta alignment.
228
229 ------------
230 Dependencies
231 ------------
232 ReadSeq
233 readseq_ 2.1.30, Conda version
234
235 .. _readseq: https://anaconda.org/bioconda/readseq
236
237 ----------
238 Input file
239 ----------
240
241 Fasta file
242 The input data file contains sequence alignment(s)
243
244
245 ---------
246 Parameter
247 ---------
248
249 Output name
250 Output base name for the ouput files
251
252
253 ------------
254 Output files
255 ------------
256
257 Output_name
258 Resulting tree in phylip format
259
260 Output_name.log
261 Log file
262
263 ---------------------------------------------------
264
265 ---------------
266 Working example
267 ---------------
268
269 Input file
270 ==========
271
272 Fasta file
273 -----------
274
275 ::
276
277 >IRAT112 GAGAACCGTCCTGTAAGTACTCTTGCTTTAAGTAATAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATTATCATTATGAATCAATAAACAACTTGATGTTGTGCTCCATGTACGATATATAAAGACAGATA
278 >KARASUKARASURANKASU GAGAACCGTCCTGTAAGTACTCTTGCTTTAAATACGAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATGTTCATCATGAATCTATAGTTAACTTGATGTTGTGCTCCATGTACGATATAAAAAGTTAGATA
279
280
281 Parameters
282 ==========
283
284 Output name -> phylip conversion
285
286
287 Output file
288 ===========
289
290 phylip conversion
291 -----------------
292
293 ::
294
295 168 5125
296 IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
297 KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT
298
299 ]]></help>
300 <citations>
301 <citation type="doi" >10.1002/0471250953.bia01es00</citation>
302 </citations>
303
304 </tool>