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Imported from capsule None
author iuc
date Thu, 21 May 2015 03:58:09 -0400
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-1:000000000000 0:fae6527990af
1 <tool id="vsearch_search" name="VSearch search" version="@VERSION@.0">
2 <description></description>
3 <macros>
4 <import>vsearch_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command>
10 <![CDATA[
11 vsearch
12
13 @GENERAL@
14 --db $dbfile
15 --dbmask $dbmask
16
17 ##--fulldp full dynamic programming alignment (always on)
18 ##--gapext STRING penalties for gap extension (2I/1E)
19 ##--gapopen STRING penalties for gap opening (20I/2E)
20 $hardmask
21 --id $id
22 --iddef $iddef
23
24 #if $qmask != 'no':
25 --qmask $qmask
26 #end if
27
28 ## --rowlen INT width of alignment lines in alnout output (64)
29
30 $self_param
31 $selfid_param
32 #if $sizeout:
33 --sizeout $sizeout
34 #end if
35 --strand $strand
36 --usearch_global $queryfile
37
38 #if '--alnout' in str($outputs):
39 --alnout $alnout
40 #end if
41 #if '--blast6out' in str($outputs):
42 --blast6out $blast6out
43 #end if
44 #if '--dbmatched' in str($outputs):
45 --dbmatched $dbmatched
46 #end if
47 #if '--dbnotmatched' in str($outputs):
48 --dbnotmatched $dbnotmatched
49 #end if
50 #if '--fastapairs' in str($outputs):
51 --fastapairs $fastapairs
52 #end if
53 #if '--notmatched' in str($outputs):
54 --notmatched $notmatched
55 #end if
56 #if '--matched' in str($outputs):
57 --matched $matched
58 #end if
59
60 #if $adv_opts.adv_opts_selector == "advanced":
61 $adv_opts.top_hits_only
62 $adv_opts.rightjust
63 $adv_opts.leftjust
64 --target_cov $adv_opts.target_cov
65 --query_cov $adv_opts.query_cov
66
67
68 #if $adv_opts.maxid:
69 --maxid $adv_opts.maxid
70 #end if
71 #if $adv_opts.maxqt:
72 --maxqt $adv_opts.maxqsize
73 #end if
74 #if $adv_opts.maxsizeratio:
75 --maxsizeratio $adv_opts.maxsizeratio
76 #end if
77 #if $adv_opts.maxsl:
78 --maxsl $adv_opts.maxsl
79 #end if
80 #if $adv_opts.mid:
81 --mid $adv_opts.mid
82 #end if
83 #if $adv_opts.minqt:
84 --minqt $adv_opts.minqt
85 #end if
86 #if $adv_opts.minsizeratio:
87 --minsizeratio $adv_opts.minseqlength
88 #end if
89 #if $adv_opts.minsl:
90 --minsl $adv_opts.minsl
91 #end if
92
93 #if $adv_opts.mintsize:
94 --mintsize $adv_opts.mintsize
95 #end if
96 #if $adv_opts.mismatch:
97 --mismatch $adv_opts.mismatch
98 #end if
99 #if $adv_opts.maxqsize:
100 --maxqsize $adv_opts.maxqsize
101 #end if
102 #if $adv_opts.mincols:
103 --mincols $adv_opts.mincols
104 #end if
105 #if $adv_opts.maxsubs:
106 --maxsubs $adv_opts.maxsubs
107 #end if
108 #if $adv_opts.maxrejects:
109 --maxrejects $adv_opts.maxrejects
110 #end if
111 #if $adv_opts.maxaccepts:
112 --maxaccepts $adv_opts.maxaccepts
113 #end if
114 #if $adv_opts.maxdiffs:
115 --maxdiffs $adv_opts.maxdiffs
116 #end if
117 #if $adv_opts.maxgaps:
118 --maxgaps $adv_opts.maxgaps
119 #end if
120 #if $adv_opts.maxhits:
121 --maxhits $adv_opts.maxhits
122 #end if
123 #if $adv_opts.match:
124 --match $adv_opts.match
125 #end if
126 #if $adv_opts.idprefix:
127 --idprefix $adv_opts.idprefix
128 #end if
129 #if $adv_opts.idsuffix:
130 --idsuffix $adv_opts.idsuffix
131 #end if
132
133 #if $adv_opts.uclust_output.uclust_output_select == 'yes':
134 --uc
135 $adv_opts.uclust_output.uc_allhits
136 #end if
137
138 #if $adv_opts.userfields_output.userfields_output_select == 'yes':
139 --userfields '#echo '+'.join( str($adv_opts.userfields_output.userfields).split(',') )#'
140 --userout $userout
141 #end if
142
143 ##--weak_id REAL include aligned hits with >= id; continue search
144 --wordlength $adv_opts.wordlength
145
146 $$adv_opts.output_no_hits
147
148 #end if
149
150
151 ]]>
152 </command>
153 <inputs>
154 <param name="queryfile" type="data" format="fasta" label="Select your query FASTA file" help="(--usearch_global)" />
155 <param name="dbfile" type="data" format="fasta" label="Select your database FASTA file" help="(--db)" />
156
157 <expand macro="qmask" />
158 <expand macro="sizeout" />
159 <expand macro="strand" />
160 <expand macro="self_and_selfid" />
161 <expand macro="id_and_iddef" />
162 <expand macro="hardmask" />
163
164 <param name="dbmask" type="select" optional="True" label="Mask database sequences" help="(--dbmask)">
165 <option value="none" selected="True">No masking</option>
166 <option value="dust" selected="True">dust</option>
167 <option value="soft">soft</option>
168 </param>
169
170 <expand macro="general_output">
171 <option value="--dbmatched">FASTA file for matching database sequences</option>
172 <option value="--dbnotmatched">FASTA file for non-matching database sequences</option>
173 <option value="--notmatched">Write non-matching query sequences to separate file</option>
174 <option value="--matched">Write matching query sequences to separate file</option>
175 </expand>
176
177 <conditional name="adv_opts">
178 <param name="adv_opts_selector" type="select" label="Advanced Options">
179 <option value="basic" selected="True">Hide Advanced Options</option>
180 <option value="advanced">Show Advanced Options</option>
181 </param>
182 <when value="basic" />
183 <when value="advanced">
184
185 <param name="top_hits_only" type="boolean" truevalue="--top_hits_only" falsevalue="" checked="False"
186 label="Output only hits with identity equal to the best" help="(--top_hits_only)"/>
187 <param name="rightjust" type="boolean" truevalue="--rightjust" falsevalue="" checked="False"
188 label="Reject if terminal gaps at alignment right end" help="(--rightjust)"/>
189 <param name="leftjust" type="boolean" truevalue="--leftjust" falsevalue="" checked="False"
190 label="Reject if terminal gaps at alignment left end" help="(--leftjust)"/>
191
192 <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value"
193 help="(--query_cov)"/>
194 <param name="target_cov" type="float" value="" optional="True" label="Reject if fraction of target seq. aligned lower than this value"
195 help="(--target_cov)"/>
196 <param name="maxid" type="float" value="" optional="True" label="Reject if identity higher than this value"
197 help="(--maxid)"/>
198 <param name="maxqt" type="float" value="" optional="True" label="Reject if query/target length ratio higher than this value"
199 help="(--maxqt)"/>
200 <param name="maxsizeratio" type="float" value="" optional="True" label="Reject if query/target abundance ratio higher than this value"
201 help="(--maxsizeratio)"/>
202 <param name="maxsl" type="float" value="" optional="True" label="Reject if shorter/longer length ratio higher than this value"
203 help="(--maxsl)"/>
204 <param name="mid" type="float" value="" optional="True" label="Reject if percent identity lower than this value, ignoring gaps"
205 help="(--mid)"/>
206 <param name="minqt" type="float" value="" optional="True" label="Reject if query/target length ratio lower than this value"
207 help="(--minqt)"/>
208 <param name="minsl" type="float" value="" optional="True" label="Reject if shorter/longer length ratio lower than this value"
209 help="(--minsl)"/>
210 <param name="minsizeratio" type="float" value="" optional="True" label="Reject if query/target abundance ratio lower than this value"
211 help="(--minsizeratio)"/>
212
213 <param name="maxqsize" type="integer" value="" optional="True" label="Reject if query abundance larger than this value"
214 help="(--maxqsize)"/>
215 <param name="mincols" type="integer" value="" optional="True" label="Reject if alignment length shorter than this value"
216 help="(--mincols)"/>
217 <param name="maxsubs" type="integer" value="" optional="True" label="Reject if more substitutions than this value"
218 help="(--maxsubs)"/>
219 <expand macro="maxrejects" />
220 <expand macro="maxaccepts" />
221 <param name="maxdiffs" type="integer" value="" optional="True" label="Reject if more substitutions or indels than this value"
222 help="(--maxdiffs)"/>
223 <param name="maxgaps" type="integer" value="" optional="True" label="Reject if more indels than this value"
224 help="(--maxgaps)"/>
225 <param name="maxhits" type="integer" value="" optional="True" label="Maximum number of hits to show"
226 help="(--maxhits)"/>
227 <param name="match" type="integer" value="2" label="Score for match"
228 help="(--match)"/>
229 <param name="idprefix" type="integer" value="" optional="True" label="Reject if first n nucleotides do not match"
230 help="(--idprefix)"/>
231 <param name="idsuffix" type="integer" value="" optional="True" label="Reject if last n nucleotides do not match"
232 help="(--idsuffix)"/>
233 <param name="mintsize" type="integer" value="" optional="True" label="Reject if target abundance lower"
234 help="(--mintsize)"/>
235 <param name="mismatch" type="integer" value="-4" label="Score for mismatch"
236 help="(--mismatch)"/>
237
238 <conditional name="uclust_output">
239 <param name="uclust_output_select" type="select" label="UCLUST-like output" help="(--uc)">
240 <option value="yes">Yes</option>
241 <option value="no" selected="True">No</option>
242 </param>
243 <when value="yes">
244 <param name="uc_allhits" type="boolean" truevalue="--uc_allhits" falsevalue="" checked="False"
245 label="Show all, not just top hits" help="(--uc_allhits)"/>
246 </when>
247 <when value="no" />
248 </conditional>
249
250 <param name="wordlength" type="integer" value="8" min="3" max="15" label="Length of words for database index 3-15"
251 help="Allowed values: 3-15 (--wordlength)"/>
252 <param name="output_no_hits" type="boolean" truevalue="--output_no_hits" falsevalue="" checked="False"
253 label="Write non-matching queries to the output file" help="(--output_no_hits)"/>
254
255 <expand macro="userfields" />
256 </when>
257 </conditional>
258
259
260 </inputs>
261 <outputs>
262 <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
263 <filter>adv_opts.uclust_output.uclust_output_select == 'yes'</filter>
264 </data>
265 <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences">
266 <filter>'--dbnotmatchedt' in outputs</filter>
267 </data>
268 <data name="dbmatched" format="fasta" label="${tool.name} on ${on_string}: Matched database sequences">
269 <filter>'--dbmatched' in outputs</filter>
270 </data>
271 <data name="alnout" format="fasta" label="${tool.name} on ${on_string}: Alignment">
272 <filter>'--alnout' in outputs</filter>
273 </data>
274 <data name="blast6out" format="tabular" label="${tool.name} on ${on_string}: BLAST like tabular">
275 <filter>'--blast6out' in outputs</filter>
276 </data>
277 <data name="notmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched queries">
278 <filter>'--notmatched' in outputs</filter>
279 </data>
280 <data name="matched" format="fasta" label="${tool.name} on ${on_string}: Matching query sequences">
281 <filter>'--matched' in outputs</filter>
282 </data>
283 <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences">
284 <filter>'--fastapairs' in outputs</filter>
285 </data>
286 <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output">
287 <filter>adv_opts.userfields_output.userfields_output_select == 'yes'</filter>
288 </data>
289 </outputs>
290 <tests>
291 <test>
292 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" />
293 <param name="queryfile" value="query.fasta" ftype="fasta" />
294 <param name="outputs" value="--blast6out,--dbmatched" />
295 <param name="dbmask" value="none" />
296 <param name="adv_opts_selector" value="advanced" />
297 <param name="top_hits_only" value="True" />
298 <output name="dbmatched" file="search_dbmatched_result1.fasta" ftype="fasta" />
299 <output name="blast6out" file="search_blast6out_result1.tabular" ftype="tabular" />
300 </test>
301 <test>
302 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" />
303 <param name="queryfile" value="query.fasta" ftype="fasta" />
304 <param name="outputs" value="--fastapairs,--matched" />
305 <param name="dbmask" value="none" />
306 <param name="adv_opts_selector" value="advanced" />
307 <param name="userfields_output_select" value="yes" />
308 <param name="userfields" value="query,target,evalue" />
309 <param name="top_hits_only" value="True" />
310 <param name="output_no_hits" value="True" />
311 <output name="matched" file="search_matched_result2.fasta" ftype="fasta" />
312 <output name="fastapairs" file="search_fastapairs_result2.fasta" ftype="fasta" />
313 <output name="userout" file="search_userfields_result2.tabular" ftype="tabular" />
314 </test>
315 </tests>
316 <help>
317 <![CDATA[
318 **What it does**
319
320 Sequence search based on vsearch.
321
322 @USERFIELDS_HELP@
323
324 Searching options
325 --alnout FILENAME filename for human-readable alignment output
326 --blast6out FILENAME filename for blast-like tab-separated output
327 --db FILENAME filename for FASTA formatted database for search
328 --dbmask mask db with "dust", "soft" or "none" method (dust)
329 --dbmatched FILENAME FASTA file for matching database sequences
330 --dbnotmatched FILENAME FASTA file for non-matching database sequences
331 --fastapairs FILENAME FASTA file with pairs of query and target
332 --fulldp full dynamic programming alignment (always on)
333 --gapext STRING penalties for gap extension (2I/1E)
334 --gapopen STRING penalties for gap opening (20I/2E)
335 --hardmask mask by replacing with N instead of lower case
336 --id REAL reject if identity lower
337 --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)
338 --idprefix INT reject if first n nucleotides do not match
339 --idsuffix INT reject if last n nucleotides do not match
340 --leftjust reject if terminal gaps at alignment left end
341 --match INT score for match (2)
342 --matched FILENAME FASTA file for matching query sequences
343 --maxaccepts INT number of hits to accept and show per strand (1)
344 --maxdiffs INT reject if more substitutions or indels
345 --maxgaps INT reject if more indels
346 --maxhits INT maximum number of hits to show (unlimited)
347 --maxid REAL reject if identity higher
348 --maxqsize INT reject if query abundance larger
349 --maxqt REAL reject if query/target length ratio higher
350 --maxrejects INT number of non-matching hits to consider (32)
351 --maxsizeratio REAL reject if query/target abundance ratio higher
352 --maxsl REAL reject if shorter/longer length ratio higher
353 --maxsubs INT reject if more substitutions
354 --mid REAL reject if percent identity lower, ignoring gaps
355 --mincols INT reject if alignment length shorter
356 --minqt REAL reject if query/target length ratio lower
357 --minsizeratio REAL reject if query/target abundance ratio lower
358 --minsl REAL reject if shorter/longer length ratio lower
359 --mintsize INT reject if target abundance lower
360 --mismatch INT score for mismatch (-4)
361 --notmatched FILENAME FASTA file for non-matching query sequences
362 --output_no_hits output non-matching queries to output files
363 --qmask mask query with "dust", "soft" or "none" method (dust)
364 --query_cov REAL reject if fraction of query seq. aligned lower
365 --rightjust reject if terminal gaps at alignment right end
366 --rowlen INT width of alignment lines in alnout output (64)
367 --self reject if labels identical
368 --selfid reject if sequences identical
369 --sizeout write abundance annotation to output
370 --strand search "plus" or "both" strands (plus)
371 --target_cov REAL reject if fraction of target seq. aligned lower
372 --top_hits_only output only hits with identity equal to the best
373 --uc FILENAME filename for UCLUST-like output
374 --uc_allhits show all, not just top hit with uc output
375 --usearch_global FILENAME filename of queries for global alignment search
376 --userfields STRING fields to output in userout file
377 --userout FILENAME filename for user-defined tab-separated output
378 --weak_id REAL include aligned hits with >= id; continue search
379 --wordlength INT length of words for database index 3-15 (8)
380
381 @EXTERNAL_DOCUMENTATION@
382
383 -------
384
385 @REFERENCES@
386
387
388 ]]>
389 </help>
390 <expand macro="citations" />
391 </tool>