Mercurial > repos > jjohnson > gmap
comparison gmap.xml @ 0:10e3476429b5 draft
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author | jjohnson |
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date | Fri, 05 Oct 2012 13:51:49 -0400 |
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children | 74391fc6e3f2 |
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1 <tool id="gmap" name="GMAP" version="2.0.1"> | |
2 <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description> | |
3 <requirements> | |
4 <requirement type="binary">gmap</requirement> | |
5 </requirements> | |
6 <version_string>gmap --version</version_string> | |
7 <command> | |
8 #import os,os.path | |
9 gmap | |
10 --nthreads=4 --ordered | |
11 #if $refGenomeSource.genomeSource == "history": | |
12 --gseg=$refGenomeSource.ownFile | |
13 #elif $refGenomeSource.genomeSource == "gmapdb": | |
14 #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0] | |
15 --dir=$refGenomeSource.gmapdb.extra_files_path --db=$gmapdb | |
16 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: | |
17 --kmer=$refGenomeSource.kmer | |
18 #end if | |
19 #else: | |
20 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) | |
21 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: | |
22 --kmer=$refGenomeSource.kmer | |
23 #end if | |
24 #end if | |
25 #if $result.format == "summary": | |
26 --summary | |
27 #elif $result.format == "align": | |
28 --align | |
29 #elif $result.format == "continuous": | |
30 --continuous | |
31 #elif $result.format == "continuous-by-exon": | |
32 --continuous-by-exon | |
33 #elif $result.format == "compress": | |
34 --compress | |
35 #elif $result.format == "exons_dna": | |
36 --exons=cdna | |
37 #elif $result.format == "exons_gen": | |
38 --exons=genomic | |
39 #elif $result.format == "protein_dna": | |
40 --protein_dna | |
41 #elif $result.format == "protein_gen": | |
42 --protein_gen | |
43 #elif $result.format == "sam": | |
44 --format=$result.sam_paired_read | |
45 $result.no_sam_headers | |
46 #* Removed in gmap version 2011-11-30 | |
47 #if len($result.noncanonical_splices.__str__) > 0 | |
48 --noncanonical-splices=$result.noncanonical_splices | |
49 #end if | |
50 *# | |
51 #if len($result.read_group_id.__str__) > 0 | |
52 --read-group-id=$result.read_group_id | |
53 #end if | |
54 #if len($result.read_group_name.__str__) > 0 | |
55 --read-group-name=$result.read_group_name | |
56 #end if | |
57 #if len($result.read_group_library.__str__) > 0 | |
58 --read-group-library=$result.read_group_library | |
59 #end if | |
60 #if len($result.read_group_platform.__str__) > 0 | |
61 --read-group-platform=$result.read_group_platform | |
62 #end if | |
63 #elif $result.format != "gmap": | |
64 --format=$result.format | |
65 #end if | |
66 #if $computation.options == "advanced": | |
67 $computation.nosplicing | |
68 $computation.cross_species | |
69 #if len($computation.min_intronlength.__str__) > 0 | |
70 --min-intronlength=$computation.min_intronlength | |
71 #end if | |
72 #if len($computation.intronlength.__str__) > 0 | |
73 --intronlength=$computation.intronlength | |
74 #end if | |
75 #if len($computation.localsplicedist.__str__) > 0 | |
76 --localsplicedist=$computation.localsplicedist | |
77 #end if | |
78 #if len($computation.totallength.__str__) > 0 | |
79 --totallength=$computation.totallength | |
80 #end if | |
81 #if len($computation.trimendexons.__str__) > 0 | |
82 --trimendexons=$computation.trimendexons | |
83 #end if | |
84 --direction=$computation.direction | |
85 --canonical-mode=$computation.canonical | |
86 --prunelevel=$computation.prunelevel | |
87 --allow-close-indels=$computation.allow_close_indels | |
88 #if len($computation.microexon_spliceprob.__str__) >= 0: | |
89 --microexon-spliceprob=$computation.microexon_spliceprob | |
90 #end if | |
91 #if len($computation.chimera_margin.__str__) >= 0: | |
92 --chimera-margin=$computation.chimera_margin | |
93 #end if | |
94 #end if | |
95 #if $advanced.options == "used": | |
96 #if len($advanced.npaths.__str__) > 0: | |
97 --npaths=$advanced.npaths | |
98 #end if | |
99 #if len($advanced.suboptimal_score.__str__) > 0: | |
100 --suboptimal-score=$advanced.suboptimal_score | |
101 #end if | |
102 #if len($advanced.chimera_overlap.__str__) > 0: | |
103 --chimera_overlap=$advanced.chimera_overlap | |
104 #end if | |
105 $advanced.protein | |
106 $advanced.tolerant | |
107 $advanced.nolengths | |
108 $advanced.invertmode | |
109 #if len($advanced.introngap.__str__) > 0: | |
110 --introngap=$advanced.introngap | |
111 #end if | |
112 #if len($advanced.wraplength.__str__) > 0: | |
113 --wraplength=$advanced.wraplength | |
114 #end if | |
115 #end if | |
116 #if $split_output == True | |
117 $split_output | |
118 #end if | |
119 #if len($quality_protocol.__str__) > 0: | |
120 --quality-protocol=$quality_protocol | |
121 #end if | |
122 $input | |
123 #for $i in $inputs: | |
124 ${i.added_input} | |
125 #end for | |
126 #if $split_output == True | |
127 2> $gmap_stderr | |
128 #else | |
129 2> $gmap_stderr > $output | |
130 #end if | |
131 </command> | |
132 <inputs> | |
133 <!-- Input data --> | |
134 <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="<H2>Input Sequences</H2>Select an mRNA or EST dataset to map" /> | |
135 <repeat name="inputs" title="addtional mRNA or EST dataset to map"> | |
136 <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/> | |
137 </repeat> | |
138 <param name="quality_protocol" type="select" label="Protocol for input quality scores"> | |
139 <option value="">No quality scores</option> | |
140 <option value="sanger">Sanger quality scores</option> | |
141 <option value="illumina">Illumina quality scores</option> | |
142 </param> | |
143 | |
144 <!-- GMAPDB for mapping --> | |
145 <conditional name="refGenomeSource"> | |
146 <param name="genomeSource" type="select" label="<HR><H2>Map To</H2>Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> | |
147 <option value="indexed">Use a built-in index</option> | |
148 <option value="gmapdb">Use gmapdb from the history</option> | |
149 <option value="history">Use a fasta reference sequence from the history</option> | |
150 </param> | |
151 <when value="indexed"> | |
152 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> | |
153 <options from_file="gmap_indices.loc"> | |
154 <column name="uid" index="0" /> | |
155 <column name="dbkey" index="1" /> | |
156 <column name="name" index="2" /> | |
157 <column name="kmers" index="3" /> | |
158 <column name="maps" index="4" /> | |
159 <column name="snps" index="5" /> | |
160 <column name="value" index="6" /> | |
161 </options> | |
162 </param> | |
163 <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> | |
164 <options from_file="gmap_indices.loc"> | |
165 <column name="name" index="3"/> | |
166 <column name="value" index="3"/> | |
167 <filter type="param_value" ref="gmapindex" column="6"/> | |
168 <filter type="multiple_splitter" column="3" separator=","/> | |
169 <filter type="add_value" name="" value=""/> | |
170 <filter type="sort_by" column="3"/> | |
171 </options> | |
172 </param> | |
173 <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" help=""> | |
174 <options from_file="gmap_indices.loc"> | |
175 <column name="name" index="4"/> | |
176 <column name="value" index="4"/> | |
177 <filter type="param_value" ref="gmapindex" column="6"/> | |
178 <filter type="multiple_splitter" column="4" separator=","/> | |
179 <filter type="add_value" name="" value=""/> | |
180 <filter type="sort_by" column="4"/> | |
181 </options> | |
182 </param> | |
183 </when> | |
184 <when value="gmapdb"> | |
185 <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" | |
186 help="A GMAP database built with GMAP Build"/> | |
187 <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> | |
188 <options> | |
189 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> | |
190 </options> | |
191 </param> | |
192 <param name="map" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> | |
193 <options> | |
194 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> | |
195 </options> | |
196 </param> | |
197 </when> | |
198 <when value="history"> | |
199 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" | |
200 help="Fasta containing genomic DNA sequence"/> | |
201 </when> | |
202 </conditional> | |
203 | |
204 | |
205 <!-- Computation options --> | |
206 <conditional name="computation"> | |
207 <param name="options" type="select" label="<HR>Computational Settings" help=""> | |
208 <option value="default">Use default settings</option> | |
209 <option value="advanced">Set Computation Options</option> | |
210 </param> | |
211 <when value="default"/> | |
212 <when value="advanced"> | |
213 <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/> | |
214 <param name="min_intronlength" type="integer" value="" optional="true" label="Min length for one internal intron (default 9)." help="Below this size, a genomic gap will be considered a deletion rather than an intron." > | |
215 <validator type="in_range" message="min_intronlength must be positive" min="0" /> | |
216 </param> | |
217 <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" > | |
218 <validator type="in_range" message="intronlength must be positive" min="0" /> | |
219 </param> | |
220 <param name="localsplicedist" type="integer" value="" optional="true" label="Max length for known splice sites at ends of sequence (default 200000)" > | |
221 <validator type="in_range" message="localsplicedist must be positive" min="0" /> | |
222 </param> | |
223 <param name="totallength" type="integer" value="" optional="true" label="Max total intron length (default 2400000)" > | |
224 <validator type="in_range" message="totallength must be positive" min="0" /> | |
225 </param> | |
226 <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera" | |
227 help=" default is 40, To turn off, set to a large value (greater than the query length)" > | |
228 <validator type="in_range" message="chimera_margin must be positive" min="0" /> | |
229 </param> | |
230 <param name="direction" type="select" label="cDNA direction"> | |
231 <option value="auto">auto</option> | |
232 <option value="sense_force">sense_force</option> | |
233 <option value="antisense_force">antisense_force</option> | |
234 <option value="sense_filter">sense_filter</option> | |
235 <option value="antisense_filter">antisense_filter</option> | |
236 </param> | |
237 <param name="trimendexons" type="integer" value="" optional="true" label="Trim end exons with fewer than given number of matches (in nt, default 12)" > | |
238 <validator type="in_range" message="trimendexons must be positive" min="1" /> | |
239 </param> | |
240 <param name="cross_species" type="boolean" truevalue="--cross-species" falsevalue="" checked="false" label="Cross-species alignment" help="For cross-species alignments, use a more sensitive search for canonical splicing"/> | |
241 | |
242 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns"> | |
243 <option value="1">high reward (default)</option> | |
244 <option value="0">low reward</option> | |
245 <option value="2">low reward for high-identity sequences</option> | |
246 </param> | |
247 <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other"> | |
248 <option value="1" selected="true">yes (default)</option> | |
249 <option value="0">no</option> | |
250 <option value="2">only for high-quality alignments</option> | |
251 </param> | |
252 <param name="microexon_spliceprob" type="float" value="" optional="true" label="Micro Exon splice probablility threshold" | |
253 help="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" > | |
254 <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/> | |
255 </param> | |
256 <param name="prunelevel" type="select" label="Pruning level"> | |
257 <option value="0">no pruning (default)</option> | |
258 <option value="1">poor sequences</option> | |
259 <option value="2">repetitive sequences</option> | |
260 <option value="3">poor and repetitive sequences</option> | |
261 </param> | |
262 <!-- could do this as a config file | |
263 <param name="chrsubsetfile" type="data" format="fasta" label="User-supplied chromosome subset file" /> | |
264 <param name="chrsubset" type="text" label="Chromosome subset to search" /> | |
265 --> | |
266 </when> | |
267 </conditional> | |
268 | |
269 <!-- Advanced Settings --> | |
270 <conditional name="advanced"> | |
271 <param name="options" type="select" label="<HR>Advanced Settings" help=""> | |
272 <option value="default">Use default settings</option> | |
273 <option value="used">Set Options</option> | |
274 </param> | |
275 <when value="default"/> | |
276 <when value="used"> | |
277 <param name="nolengths" type="boolean" checked="false" truevalue="--nolengths=true" falsevalue="" label="No intron lengths in alignment"/> | |
278 <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help=""> | |
279 <option value="">Don't invert the cDNA (default)</option> | |
280 <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option> | |
281 <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option> | |
282 </param> | |
283 <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)"> | |
284 <validator type="in_range" message="introngap must be positive" min="0" /> | |
285 </param> | |
286 <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)"> | |
287 <validator type="in_range" message="wraplength must be positive" min="1" /> | |
288 </param> | |
289 <param name="npaths" type="integer" value="" optional="true" | |
290 label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." > | |
291 <validator type="in_range" message="npaths must be positive" min="0" /> | |
292 </param> | |
293 <param name="suboptimal_score" type="integer" value="" optional="true" | |
294 label="Report only paths whose score is within this value of the best path" | |
295 help="By default the program prints all paths found." > | |
296 <validator type="in_range" message="suboptimal_score must be positive" min="0" /> | |
297 </param> | |
298 <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" > | |
299 <validator type="in_range" message="chimera_overlap must be positive" min="0" /> | |
300 </param> | |
301 <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" | |
302 label="Translates cDNA with corrections for frameshifts"/> | |
303 <param name="protein" type="select" label="Protein alignment" help=""> | |
304 <option value="">default</option> | |
305 <option value="--fulllength=true">Assume full-length protein, starting with Met</option> | |
306 <option value="--truncate=true">Truncate alignment around full-length protein, Met to Stop</option> | |
307 </param> | |
308 </when> | |
309 </conditional> | |
310 | |
311 <!-- Output data --> | |
312 <conditional name="result"> | |
313 <param name="format" type="select" label="<HR><H2>Output</H2>Select the output format" help=""> | |
314 <option value="gmap">GMAP default output</option> | |
315 <option value="summary">Summary of alignments</option> | |
316 <option value="align">Alignment</option> | |
317 <option value="continuous">Alignment in three continuous lines</option> | |
318 <option value="continuous-by-exon">Alignment in three lines per exon</option> | |
319 <option value="compress">Print output in compressed format</option> | |
320 <option value="exons_dna">Print exons cDNA</option> | |
321 <option value="exons_gen">Print exons genomic</option> | |
322 <option value="protein_dna">Print protein sequence (cDNA)</option> | |
323 <option value="protein_gen">Print protein sequence (genomic)</option> | |
324 <option value="psl">PSL (BLAT) format</option> | |
325 <option value="gff3_gene">GFF3 gene format</option> | |
326 <option value="gff3_match_cdna">GFF3 match cDNA format</option> | |
327 <option value="gff3_match_est">GFF3 match EST format</option> | |
328 <option value="splicesites">splicesites output (for GSNAP)</option> | |
329 <option value="introns">introns output (for GSNAP)</option> | |
330 <option value="map_exons">IIT FASTA exon map format</option> | |
331 <option value="map_genes">IIT FASTA map format</option> | |
332 <option value="coords">coords in table format</option> | |
333 <option value="sam" selected="true">SAM format</option> | |
334 </param> | |
335 <when value="gmap"> | |
336 </when> | |
337 <when value="summary"/> | |
338 <when value="align"> | |
339 </when> | |
340 <when value="continuous"> | |
341 </when> | |
342 <when value="continuous-by-exon"> | |
343 </when> | |
344 <when value="compress"/> | |
345 <when value="exons_dna"/> | |
346 <when value="exons_gen"/> | |
347 <when value="protein_dna"/> | |
348 <when value="protein_gen"/> | |
349 <when value="psl"/> | |
350 <when value="gff3_gene"/> | |
351 <when value="gff3_match_cdna"/> | |
352 <when value="gff3_match_est"/> | |
353 <when value="splicesites"/> | |
354 <when value="introns"/> | |
355 <when value="map_exons"/> | |
356 <when value="map_genes"/> | |
357 <when value="coords"/> | |
358 <when value="sam"> | |
359 <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/> | |
360 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> | |
361 <!-- Removed in gmap version 2011-11-30 | |
362 <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING."> | |
363 <option value="">Use default</option> | |
364 <option value="N">N</option> | |
365 <option value="D">D</option> | |
366 </param> | |
367 --> | |
368 <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/> | |
369 <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/> | |
370 <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/> | |
371 <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/> | |
372 </when> | |
373 </conditional> <!-- name="result" --> | |
374 | |
375 <param name="split_output" type="boolean" truevalue="--split-output=gmap_out" falsevalue="" checked="false" label="Separate outputs for nomapping, uniq, mult, and chimera" help="(chimera only when chimera-margin is selected)"/> | |
376 | |
377 | |
378 <!-- | |
379 map=iitfile Map file. If argument is '?' (with the quotes), this lists available map files. | |
380 mapexons Map each exon separately | |
381 mapboth Report hits from both strands of genome | |
382 flanking=INT Show flanking hits (default 0) | |
383 print-comment Show comment line for each hit | |
384 --> | |
385 | |
386 | |
387 </inputs> | |
388 <outputs> | |
389 <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/> | |
390 <data format="txt" name="output" label="${tool.name} on ${on_string} ${result.format}" > | |
391 <filter>(split_output == False)</filter> | |
392 <change_format> | |
393 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
394 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
395 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
396 <when input="result['format']" value="sam" format="sam"/> | |
397 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
398 <when input="result['format']" value="introns" format="gmap_introns"/> | |
399 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
400 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
401 </change_format> | |
402 </data> | |
403 <data format="txt" name="uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gmap_out.uniq"> | |
404 <filter>(split_output == True)</filter> | |
405 <change_format> | |
406 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
407 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
408 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
409 <when input="result['format']" value="sam" format="sam"/> | |
410 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
411 <when input="result['format']" value="introns" format="gmap_introns"/> | |
412 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
413 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
414 </change_format> | |
415 </data> | |
416 <data format="txt" name="transloc" label="${tool.name} on ${on_string} transloc.${result.format}" from_work_dir="gmap_out.transloc"> | |
417 <filter>(split_output == True)</filter> | |
418 <change_format> | |
419 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
420 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
421 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
422 <when input="result['format']" value="sam" format="sam"/> | |
423 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
424 <when input="result['format']" value="introns" format="gmap_introns"/> | |
425 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
426 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
427 </change_format> | |
428 </data> | |
429 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gmap_out.nomapping"> | |
430 <filter>(split_output == True)</filter> | |
431 <change_format> | |
432 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
433 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
434 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
435 <when input="result['format']" value="sam" format="sam"/> | |
436 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
437 <when input="result['format']" value="introns" format="gmap_introns"/> | |
438 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
439 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
440 </change_format> | |
441 </data> | |
442 <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}" from_work_dir="gmap_out.mult"> | |
443 <filter>(split_output == True)</filter> | |
444 <change_format> | |
445 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
446 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
447 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
448 <when input="result['format']" value="sam" format="sam"/> | |
449 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
450 <when input="result['format']" value="introns" format="gmap_introns"/> | |
451 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
452 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
453 </change_format> | |
454 </data> | |
455 </outputs> | |
456 <tests> | |
457 </tests> | |
458 | |
459 <help> | |
460 | |
461 **What it does** | |
462 | |
463 GMAP_ (Genomic Mapping and Alignment Program) The functionality provided by gmap allows a user to: (1) map and align a single cDNA interactively against a large genome in about a second, without the startup time of several minutes typically needed by existing mapping programs; (2) switch arbitrarily among different genomes, without the need for a preloaded server dedicated to each genome; (3) run the program on computers with as little as 128 MB of RAM (random access memory); (4) perform high-throughput batch processing of cDNAs by using memory mapping and multithreading when appropriate memory and hardware are available; (5) generate accurate gene models, even in the presence of substantial polymorphisms and sequence errors; (6) locate splice sites accurately without the use of probabilistic splice site models, allowing generalized use of the program across species; (7) detect statistically significant microexons and incorporate them into the alignment; and (8) handle mapping and alignment tasks on genomes having alternate assemblies, linkage groups or strains. It is developed by Thomas D. Wu of Genentech, Inc. | |
464 | |
465 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 | |
466 | |
467 .. _GMAP: http://research-pub.gene.com/gmap/ | |
468 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 | |
469 | |
470 ------ | |
471 | |
472 **Know what you are doing** | |
473 | |
474 .. class:: warningmark | |
475 | |
476 You will want to read the README_ | |
477 | |
478 .. _README: http://research-pub.gene.com/gmap/src/README | |
479 | |
480 </help> | |
481 </tool> | |
482 |