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comparison gsnap.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
comparison
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7:561503a442f0 8:a89fec682254
1 <tool id="gsnap" name="GSNAP" version="2.0.0"> 1 <tool id="gsnap" name="GSNAP" version="2.0.1">
2 <description>Genomic Short-read Nucleotide Alignment Program</description> 2 <description>Genomic Short-read Nucleotide Alignment Program</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">gsnap</requirement> 4 <requirement type="binary">gsnap</requirement>
5 <!-- proposed tag for added datatype dependencies -->
6 <requirement type="datatype">gmapdb</requirement>
7 <requirement type="datatype">gmapsnpindex</requirement>
8 <requirement type="datatype">splicesites.iit</requirement>
9 <requirement type="datatype">introns.iit</requirement>
10 </requirements> 5 </requirements>
11 <version_string>gsnap --version</version_string> 6 <version_string>gsnap --version</version_string>
12 <command> 7 <command>
13 #import os.path, re 8 #import os.path, re
14 gsnap 9 gsnap
23 --kmer=$refGenomeSource.kmer 18 --kmer=$refGenomeSource.kmer
24 #end if 19 #end if
25 #if $refGenomeSource.use_splicing.src == 'gmapdb': 20 #if $refGenomeSource.use_splicing.src == 'gmapdb':
26 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: 21 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:
27 -s $refGenomeSource.use_splicing.splicemap.value 22 -s $refGenomeSource.use_splicing.splicemap.value
23 #if $computation.trim_mismatch_score.__str__ == '0':
24 $ambig_splice_noclip
25 #end if
28 #end if 26 #end if
29 #elif $refGenomeSource.use_splicing.src == 'history': 27 #elif $refGenomeSource.use_splicing.src == 'history':
30 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: 28 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:
31 -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap) 29 -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap)
30 #if $computation.trim_mismatch_score.__str__ == '0':
31 $ambig_splice_noclip
32 #end if
32 #end if 33 #end if
33 #end if 34 #end if
34 #if $refGenomeSource.use_snps.src == 'gmapdb': 35 #if $refGenomeSource.use_snps.src == 'gmapdb':
35 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: 36 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:
36 -v $refGenomeSource.use_snps.snpindex.value 37 -v $refGenomeSource.use_snps.snpindex.value
41 #end if 42 #end if
42 #end if 43 #end if
43 #if $refGenomeSource.mode.__str__ != '': 44 #if $refGenomeSource.mode.__str__ != '':
44 --mode=$refGenomeSource.mode 45 --mode=$refGenomeSource.mode
45 #end if 46 #end if
47 #* ## No longer in options as of version 2011-11-30
46 #if $mapq_unique_score.__str__ != '': 48 #if $mapq_unique_score.__str__ != '':
47 --mapq-unique-score=$mapq_unique_score 49 --mapq-unique-score=$mapq_unique_score
48 #end if 50 #end if
51 *#
49 #if $computation.options == "advanced": 52 #if $computation.options == "advanced":
50 #if $computation.max_mismatches.__str__ != '': 53 #if $computation.max_mismatches.__str__ != '':
51 --max-mismatches=$computation.max_mismatches 54 --max-mismatches=$computation.max_mismatches
52 #end if 55 #end if
53 $computation.query_unk_mismatch 56 $computation.query_unk_mismatch
79 #if $computation.adapter_strip.__str__ != '': 82 #if $computation.adapter_strip.__str__ != '':
80 --adapter-strip=$computation.adapter_strip 83 --adapter-strip=$computation.adapter_strip
81 #end if 84 #end if
82 #if $computation.trim_mismatch_score.__str__ != '': 85 #if $computation.trim_mismatch_score.__str__ != '':
83 --trim-mismatch-score=$computation.trim_mismatch_score 86 --trim-mismatch-score=$computation.trim_mismatch_score
87 #end if
88 #if $computation.trim_indel_score.__str__ != '':
89 --trim-indel-score=$computation.trim_indel_score
84 #end if 90 #end if
85 ## TODO - do we need these options (Is it tally XOR runlength?): 91 ## TODO - do we need these options (Is it tally XOR runlength?):
86 ## --tallydir= --use-tally=tally 92 ## --tallydir= --use-tally=tally
87 ## --runlengthdir --use-runlength=runlength 93 ## --runlengthdir --use-runlength=runlength
88 #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0: 94 #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0:
203 #if $seq.paired.pairmax_dna.__str__ != '': 209 #if $seq.paired.pairmax_dna.__str__ != '':
204 --pairmax-dna=$seq.paired.pairmax_dna 210 --pairmax-dna=$seq.paired.pairmax_dna
205 #end if 211 #end if
206 #if $seq.paired.pairmax_rna.__str__ != '': 212 #if $seq.paired.pairmax_rna.__str__ != '':
207 --pairmax-rna=$seq.paired.pairmax_rna 213 --pairmax-rna=$seq.paired.pairmax_rna
214 #end if
215 #if $seq.paired.pairexpect.__str__ != '':
216 --pairexpect=$seq.paired.pairexpect
217 #end if
218 #if $seq.paired.pairdev.__str__ != '':
219 --pairdev=$seq.paired.pairdev
208 #end if 220 #end if
209 $seq.fastq $seq.paired.fastq 221 $seq.fastq $seq.paired.fastq
210 #else 222 #else
211 $seq.fastq 223 $seq.fastq
212 #end if 224 #end if
243 <option value="FR">fwd-rev, typical Illumina default</option> 255 <option value="FR">fwd-rev, typical Illumina default</option>
244 <option value="RF">rev-fwd, for circularized inserts</option> 256 <option value="RF">rev-fwd, for circularized inserts</option>
245 <option value="FF">fwd-fwd, same strand</option> 257 <option value="FF">fwd-fwd, same strand</option>
246 </param> 258 </param>
247 <param name="pairmax_dna" type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/> 259 <param name="pairmax_dna" type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/>
248 <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used novelspliceing is specified or a splice file is provided. Should probably match the value for localsplicedist."/> 260 <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used when novel splicing is specified or a splice file is provided. Should probably match the value for localsplicedist."/>
261 <param name="pairexpect" type="integer" value="" optional="true" label="Expected paired-end length"
262 help="Used for calling splices in medial part of paired-end reads (default 200)"/>
263 <param name="pairdev" type="integer" value="" optional="true" label="Allowable deviation from expected paired-end length"
264 help="Used for calling splices in medial part of paired-end reads (default 25)"/>
249 </when> 265 </when>
250 </conditional> 266 </conditional>
251 <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" /> 267 <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" />
252 <param name="fastq_id_start" type="integer" value="" optional="true" label="Starting field of identifier in FASTQ header, whitespace-delimited, starting from 1" /> 268 <param name="fastq_id_start" type="integer" value="" optional="true" label="Starting field of identifier in FASTQ header, whitespace-delimited, starting from 1" />
253 <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, whitespace-delimited, starting from 1" 269 <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, whitespace-delimited, starting from 1"
279 <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/> 295 <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/>
280 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/> 296 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/>
281 </when> 297 </when>
282 298
283 </conditional> 299 </conditional>
300 <!-- No longer in options as of version 2011-11-30
284 <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold" 301 <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold"
285 help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this 302 help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this
286 (if not selected, then reports all multiple results, up to npaths)" /> 303 (if not selected, then reports all multiple results, up to npaths)" />
304 -->
287 305
288 <!-- GMAPDB for alignment --> 306 <!-- GMAPDB for alignment -->
289 <conditional name="refGenomeSource"> 307 <conditional name="refGenomeSource">
290 <param name="genomeSource" type="select" label="&lt;HR&gt;&lt;H2&gt;Align To&lt;/H2&gt;Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 308 <param name="genomeSource" type="select" label="&lt;HR&gt;&lt;H2&gt;Align To&lt;/H2&gt;Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
291 <option value="indexed">Use a built-in index</option> 309 <option value="indexed">Use a built-in index</option>
403 </param> 421 </param>
404 <when value="none"/> 422 <when value="none"/>
405 <when value="history"> 423 <when value="history">
406 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" 424 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map"
407 help="built with GMAP IIT"/> 425 help="built with GMAP IIT"/>
426 <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
427 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.
428 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
408 </when> 429 </when>
409 <when value="gmapdb"> 430 <when value="gmapdb">
410 <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> 431 <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help="">
411 <options> 432 <options>
412 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> 433 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/>
413 </options> 434 </options>
414 </param> 435 </param>
436 <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
437 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.
438 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
415 </when> 439 </when>
416 </conditional> 440 </conditional>
417 441
418 <conditional name="use_snps"> 442 <conditional name="use_snps">
419 <param name="src" type="select" label="&lt;HR&gt;Known SNPs" help="for SNP tolerant alignments"> 443 <param name="src" type="select" label="&lt;HR&gt;Known SNPs" help="for SNP tolerant alignments">
455 to align reads extending past the ends of an exon."> 479 to align reads extending past the ends of an exon.">
456 <validator type="in_range" message="The mismatches must >= 0." min="0."/> 480 <validator type="in_range" message="The mismatches must >= 0." min="0."/>
457 </param> 481 </param>
458 <param name="query_unk_mismatch" type="boolean" checked="false" truevalue="--query-unk-mismatch=1" falsevalue="" label="Count unknown (N) characters in the query as a mismatch"/> 482 <param name="query_unk_mismatch" type="boolean" checked="false" truevalue="--query-unk-mismatch=1" falsevalue="" label="Count unknown (N) characters in the query as a mismatch"/>
459 <param name="genome_unk_mismatch" type="boolean" checked="true" truevalue="" falsevalue="--genome-unk-mismatch=0" label="Count unknown (N) characters in the genome as a mismatch"/> 483 <param name="genome_unk_mismatch" type="boolean" checked="true" truevalue="" falsevalue="--genome-unk-mismatch=0" label="Count unknown (N) characters in the genome as a mismatch"/>
460 <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 3)" 484 <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 2)"
461 help="(from one end of the read to the best possible position at the other end). To turn off terminal alignments, set this to a high value." /> 485 help="(from one end of the read to the best possible position at the other end). For example, if this value is 2, then if GSNAP finds an exact or
486 1-mismatch alignment, it will not try to find a terminal alignment.
487 Note that this default value may not be low enough if you want to
488 obtain terminal alignments for very short reads, although such reads
489 probably don't have enough specificity for terminal alignments anyway." />
462 <param name="indel_penalty" type="integer" value="" optional="true" label="Penalty for an indel (default 2)" 490 <param name="indel_penalty" type="integer" value="" optional="true" label="Penalty for an indel (default 2)"
463 help="Counts against mismatches allowed. To find indels, make indel-penalty less than or equal to max-mismatches. A value &lt; 2 can lead to false positives at read ends" /> 491 help="Counts against mismatches allowed. To find indels, make indel-penalty less than or equal to max-mismatches. A value &lt; 2 can lead to false positives at read ends" />
464 <param name="indel_endlength" type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" /> 492 <param name="indel_endlength" type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" />
465 <param name="max_middle_insertions" type="integer" value="" optional="true" label="Maximum number of middle insertions allowed (default 9)" /> 493 <param name="max_middle_insertions" type="integer" value="" optional="true" label="Maximum number of middle insertions allowed (default 9)" />
466 <param name="max_middle_deletions" type="integer" value="" optional="true" label="Maximum number of middle deletions allowed (default 30)" /> 494 <param name="max_middle_deletions" type="integer" value="" optional="true" label="Maximum number of middle deletions allowed (default 30)" />
472 help="paired removes adapters from paired-end reads if a concordant or paired alignment cannot be found from the original read"> 500 help="paired removes adapters from paired-end reads if a concordant or paired alignment cannot be found from the original read">
473 <option value="paired" selected="true">paired</option> 501 <option value="paired" selected="true">paired</option>
474 <option value="off">off</option> 502 <option value="off">off</option>
475 </param> 503 </param>
476 <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)" 504 <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)"
477 help="to turn off trimming, specify 0"/> 505 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/>
506 <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)"
507 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/>
478 <param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results" 508 <param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results"
479 help="generated by gsnap_tally and iit_store"/> 509 help="generated by gsnap_tally and iit_store"/>
480 510
481 <!-- 511 <!--
482 tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is 512 tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is