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comparison gmap.xml @ 8:a89fec682254

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gmap/gsnap updated to version 2011-11-30
author Jim Johnson <jj@umn.edu>
date Thu, 08 Dec 2011 11:00:46 -0600
parents 561503a442f0
children
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7:561503a442f0 8:a89fec682254
1 <tool id="gmap" name="GMAP" version="2.0.0"> 1 <tool id="gmap" name="GMAP" version="2.0.1">
2 <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description> 2 <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">gmap</requirement> 4 <requirement type="binary">gmap</requirement>
5 <!-- proposed tag for added datatype dependencies -->
6 <requirement type="datatype">gmapdb</requirement>
7 <requirement type="datatype">gmap_annotation</requirement>
8 <requirement type="datatype">gmap_splicesites</requirement>
9 <requirement type="datatype">gmap_introns</requirement>
10 <requirement type="datatype">gmap_snps</requirement>
11 </requirements> 5 </requirements>
12 <version_string>gmap --version</version_string> 6 <version_string>gmap --version</version_string>
13 <command> 7 <command>
14 #import os,os.path 8 #import os,os.path
15 gmap 9 gmap
47 #elif $result.format == "protein_gen": 41 #elif $result.format == "protein_gen":
48 --protein_gen 42 --protein_gen
49 #elif $result.format == "sam": 43 #elif $result.format == "sam":
50 --format=$result.sam_paired_read 44 --format=$result.sam_paired_read
51 $result.no_sam_headers 45 $result.no_sam_headers
46 #* Removed in gmap version 2011-11-30
52 #if len($result.noncanonical_splices.__str__) > 0 47 #if len($result.noncanonical_splices.__str__) > 0
53 --noncanonical-splices=$result.noncanonical_splices 48 --noncanonical-splices=$result.noncanonical_splices
54 #end if 49 #end if
50 *#
55 #if len($result.read_group_id.__str__) > 0 51 #if len($result.read_group_id.__str__) > 0
56 --read-group-id=$result.read_group_id 52 --read-group-id=$result.read_group_id
57 #end if 53 #end if
58 #if len($result.read_group_name.__str__) > 0 54 #if len($result.read_group_name.__str__) > 0
59 --read-group-name=$result.read_group_name 55 --read-group-name=$result.read_group_name
68 --format=$result.format 64 --format=$result.format
69 #end if 65 #end if
70 #if $computation.options == "advanced": 66 #if $computation.options == "advanced":
71 $computation.nosplicing 67 $computation.nosplicing
72 $computation.cross_species 68 $computation.cross_species
73 --min-intronlength=$computation.min_intronlength 69 #if len($computation.min_intronlength.__str__) > 0
74 --intronlength=$computation.intronlength 70 --min-intronlength=$computation.min_intronlength
75 --localsplicedist=$computation.localsplicedist 71 #end if
76 --totallength=$computation.totallength 72 #if len($computation.intronlength.__str__) > 0
77 --trimendexons=$computation.trimendexons 73 --intronlength=$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
78 --direction=$computation.direction 84 --direction=$computation.direction
79 --canonical-mode=$computation.canonical 85 --canonical-mode=$computation.canonical
80 --prunelevel=$computation.prunelevel 86 --prunelevel=$computation.prunelevel
81 --allow-close-indels=$computation.allow_close_indels 87 --allow-close-indels=$computation.allow_close_indels
82 --microexon-spliceprob=$computation.microexon_spliceprob 88 #if len($computation.microexon_spliceprob.__str__) >= 0:
83 #if int($computation.chimera_margin) >= 0: 89 --microexon-spliceprob=$computation.microexon_spliceprob
90 #end if
91 #if len($computation.chimera_margin.__str__) >= 0:
84 --chimera-margin=$computation.chimera_margin 92 --chimera-margin=$computation.chimera_margin
85 #end if 93 #end if
86 #end if 94 #end if
87 #if $advanced.options == "used": 95 #if $advanced.options == "used":
88 #if int($advanced.npaths) >= 0: 96 #if len($advanced.npaths.__str__) > 0:
89 --npaths=$advanced.npaths 97 --npaths=$advanced.npaths
90 #end if 98 #end if
91 #if int($advanced.chimera_overlap) > 0: 99 #if len($advanced.suboptimal_score.__str__) > 0:
100 --suboptimal-score=$advanced.suboptimal_score
101 #end if
102 #if len($advanced.chimera_overlap.__str__) > 0:
92 --chimera_overlap=$advanced.chimera_overlap 103 --chimera_overlap=$advanced.chimera_overlap
93 #end if 104 #end if
94 $advanced.protein 105 $advanced.protein
95 $advanced.tolerant 106 $advanced.tolerant
96 $advanced.nolengths 107 $advanced.nolengths
97 $advanced.invertmode 108 $advanced.invertmode
98 #if int($advanced.introngap) > 0: 109 #if len($advanced.introngap.__str__) > 0:
99 --introngap=$advanced.introngap 110 --introngap=$advanced.introngap
100 #end if 111 #end if
101 #if int($advanced.wraplength) > 0: 112 #if len($advanced.wraplength.__str__) > 0:
102 --wraplength=$advanced.wraplength 113 --wraplength=$advanced.wraplength
103 #end if 114 #end if
104 #end if 115 #end if
105 #if $split_output == True 116 #if $split_output == True
106 $split_output 117 $split_output
198 <option value="advanced">Set Computation Options</option> 209 <option value="advanced">Set Computation Options</option>
199 </param> 210 </param>
200 <when value="default"/> 211 <when value="default"/>
201 <when value="advanced"> 212 <when value="advanced">
202 <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/> 213 <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/>
203 <param name="min_intronlength" type="integer" value="9" 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." /> 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." >
204 <param name="intronlength" type="integer" value="1000000" label="Max length for one intron (default 1000000)" /> 215 <validator type="in_range" message="min_intronlength must be positive" min="0" />
205 <param name="localsplicedist" type="integer" value="200000" label="Max length for known splice sites at ends of sequence (default 200000)" /> 216 </param>
206 <param name="totallength" type="integer" value="2400000" label="Max total intron length (default 2400000)" /> 217 <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" >
207 <param name="chimera_margin" type="integer" value="40" label="Amount of unaligned sequence that triggers search for a chimera (default is 40, 0 is off)" /> 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>
208 <param name="direction" type="select" label="cDNA direction"> 230 <param name="direction" type="select" label="cDNA direction">
209 <option value="auto">auto</option> 231 <option value="auto">auto</option>
210 <option value="sense_force">sense_force</option> 232 <option value="sense_force">sense_force</option>
211 <option value="antisense_force">antisense_force</option> 233 <option value="antisense_force">antisense_force</option>
212 <option value="sense_filter">sense_filter</option> 234 <option value="sense_filter">sense_filter</option>
213 <option value="antisense_filter">antisense_filter</option> 235 <option value="antisense_filter">antisense_filter</option>
214 </param> 236 </param>
215 <param name="trimendexons" type="integer" value="12" label="Trim end exons with fewer than given number of matches (in nt, default 12)" /> 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>
216 <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"/> 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"/>
217 241
218 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns"> 242 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns">
219 <option value="1">high reward (default)</option> 243 <option value="1">high reward (default)</option>
220 <option value="0">low reward</option> 244 <option value="0">low reward</option>
223 <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other"> 247 <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other">
224 <option value="1" selected="true">yes (default)</option> 248 <option value="1" selected="true">yes (default)</option>
225 <option value="0">no</option> 249 <option value="0">no</option>
226 <option value="2">only for high-quality alignments</option> 250 <option value="2">only for high-quality alignments</option>
227 </param> 251 </param>
228 <param name="microexon_spliceprob" type="float" value="0.90" label="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" > 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)" >
229 <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/> 254 <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/>
230 </param> 255 </param>
231 <param name="prunelevel" type="select" label="Pruning level"> 256 <param name="prunelevel" type="select" label="Pruning level">
232 <option value="0">no pruning (default)</option> 257 <option value="0">no pruning (default)</option>
233 <option value="1">poor sequences</option> 258 <option value="1">poor sequences</option>
253 <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help=""> 278 <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help="">
254 <option value="">Don't invert the cDNA (default)</option> 279 <option value="">Don't invert the cDNA (default)</option>
255 <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option> 280 <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option>
256 <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option> 281 <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option>
257 </param> 282 </param>
258 <param name="introngap" type="integer" value="3" label="Nucleotides to show on each end of intron (default=3)" /> 283 <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)">
259 <param name="wraplength" type="integer" value="50" label="Line Wrap length for alignment (default=50)" /> 284 <validator type="in_range" message="introngap must be positive" min="0" />
260 <param name="npaths" type="integer" value="-1" optional="true" 285 </param>
261 label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." /> 286 <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)">
262 <param name="chimera_overlap" type="integer" value="0" label="Overlap to show, if any, at chimera breakpoint" /> 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>
263 <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" 301 <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue=""
264 label="Translates cDNA with corrections for frameshifts"/> 302 label="Translates cDNA with corrections for frameshifts"/>
265 <param name="protein" type="select" label="Protein alignment" help=""> 303 <param name="protein" type="select" label="Protein alignment" help="">
266 <option value="">default</option> 304 <option value="">default</option>
267 <option value="--fulllength=true">Assume full-length protein, starting with Met</option> 305 <option value="--fulllength=true">Assume full-length protein, starting with Met</option>
292 <option value="map_exons">IIT FASTA exon map format</option> 330 <option value="map_exons">IIT FASTA exon map format</option>
293 <option value="map_genes">IIT FASTA map format</option> 331 <option value="map_genes">IIT FASTA map format</option>
294 <option value="coords">coords in table format</option> 332 <option value="coords">coords in table format</option>
295 <option value="sam" selected="true">SAM format</option> 333 <option value="sam" selected="true">SAM format</option>
296 </param> 334 </param>
297 <when value="gmap"/> 335 <when value="gmap">
336 </when>
298 <when value="summary"/> 337 <when value="summary"/>
299 <when value="align"> 338 <when value="align">
300
301 </when> 339 </when>
302 <when value="continuous"> 340 <when value="continuous">
303 </when> 341 </when>
304 <when value="continuous-by-exon"> 342 <when value="continuous-by-exon">
305 </when> 343 </when>
318 <when value="map_genes"/> 356 <when value="map_genes"/>
319 <when value="coords"/> 357 <when value="coords"/>
320 <when value="sam"> 358 <when value="sam">
321 <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/> 359 <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/>
322 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> 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
323 <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING."> 362 <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING.">
324 <option value="">Use default</option> 363 <option value="">Use default</option>
325 <option value="N">N</option> 364 <option value="N">N</option>
326 <option value="D">D</option> 365 <option value="D">D</option>
327 </param> 366 </param>
367 -->
328 <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/> 368 <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/>
329 <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/> 369 <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/>
330 <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/> 370 <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/>
331 <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/> 371 <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/>
332 </when> 372 </when>