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comparison gmap.xml @ 2:f6ba0f12cca2 draft

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Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
author peterjc
date Wed, 28 Sep 2016 10:43:44 -0400
parents 74391fc6e3f2
children 488e9d642566
comparison
equal deleted inserted replaced
1:74391fc6e3f2 2:f6ba0f12cca2
1 <tool id="gmap" name="GMAP" version="2.0.1"> 1 <tool id="gmap" name="GMAP" version="3.0.0">
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="package" version="2011-11-30">gmap</requirement> 4 <requirement type="package" version="2013-05-09">gmap</requirement>
5 </requirements> 5 </requirements>
6 <version_string>gmap --version</version_string> 6 <version_string>gmap --version</version_string>
7 <command> 7 <command>
8 #import os,os.path 8 #import os,os.path
9 gmap 9 gmap
10 --nthreads=4 --ordered 10 --nthreads=4 --ordered
11 #if $refGenomeSource.genomeSource == "history": 11 #if $refGenomeSource.genomeSource == "history":
12 --gseg=$refGenomeSource.ownFile 12 --gseg=$refGenomeSource.ownFile
13 #elif $refGenomeSource.genomeSource == "gmapdb": 13 #elif $refGenomeSource.genomeSource == "gmapdb":
14 #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0] 14 --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name
15 --dir=$refGenomeSource.gmapdb.extra_files_path --db=$gmapdb
16 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: 15 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:
17 --kmer=$refGenomeSource.kmer 16 --kmer=$refGenomeSource.kmer
18 #end if 17 #end if
19 #else: 18 #else:
20 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) 19 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)
41 #elif $result.format == "protein_gen": 40 #elif $result.format == "protein_gen":
42 --protein_gen 41 --protein_gen
43 #elif $result.format == "sam": 42 #elif $result.format == "sam":
44 --format=$result.sam_paired_read 43 --format=$result.sam_paired_read
45 $result.no_sam_headers 44 $result.no_sam_headers
45 $result.sam_use_0M
46 $result.force_xs_dir
47 $result.md_lowercase_snp
46 #* Removed in gmap version 2011-11-30 48 #* Removed in gmap version 2011-11-30
47 #if len($result.noncanonical_splices.__str__) > 0 49 #if len($result.noncanonical_splices.__str__) > 0
48 --noncanonical-splices=$result.noncanonical_splices 50 --noncanonical-splices=$result.noncanonical_splices
49 #end if 51 #end if
50 *# 52 *#
63 #elif $result.format != "gmap": 65 #elif $result.format != "gmap":
64 --format=$result.format 66 --format=$result.format
65 #end if 67 #end if
66 #if $computation.options == "advanced": 68 #if $computation.options == "advanced":
67 $computation.nosplicing 69 $computation.nosplicing
70 $computation.find_shifted_canonical
68 $computation.cross_species 71 $computation.cross_species
69 #if len($computation.min_intronlength.__str__) > 0 72 #if len($computation.min_intronlength.__str__) > 0
70 --min-intronlength=$computation.min_intronlength 73 --min-intronlength=$computation.min_intronlength
71 #end if 74 #end if
72 #if len($computation.intronlength.__str__) > 0 75 #if len($computation.intronlength.__str__) > 0
168 <filter type="multiple_splitter" column="3" separator=","/> 171 <filter type="multiple_splitter" column="3" separator=","/>
169 <filter type="add_value" name="" value=""/> 172 <filter type="add_value" name="" value=""/>
170 <filter type="sort_by" column="3"/> 173 <filter type="sort_by" column="3"/>
171 </options> 174 </options>
172 </param> 175 </param>
176 <!--
177 basesize=INT Base size to use in genome database. If not specified, the program
178 will find the highest available base size in the genome database
179 within selected k-mer size
180 sampling=INT Sampling to use in genome database. If not specified, the program
181 will find the smallest available sampling value in the genome database
182 within selected basesize and k-mer size
183
184 -->
173 <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" help=""> 185 <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"> 186 <options from_file="gmap_indices.loc">
175 <column name="name" index="4"/> 187 <column name="name" index="4"/>
176 <column name="value" index="4"/> 188 <column name="value" index="4"/>
177 <filter type="param_value" ref="gmapindex" column="6"/> 189 <filter type="param_value" ref="gmapindex" column="6"/>
222 </param> 234 </param>
223 <param name="totallength" type="integer" value="" optional="true" label="Max total intron length (default 2400000)" > 235 <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" /> 236 <validator type="in_range" message="totallength must be positive" min="0" />
225 </param> 237 </param>
226 <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera" 238 <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)" > 239 help=" default is 40, To turn off, set to 0" >
228 <validator type="in_range" message="chimera_margin must be positive" min="0" /> 240 <validator type="in_range" message="chimera_margin must be positive" min="0" />
229 </param> 241 </param>
230 <param name="direction" type="select" label="cDNA direction"> 242 <param name="direction" type="select" label="cDNA direction">
231 <option value="auto">auto</option> 243 <option value="auto">auto</option>
232 <option value="sense_force">sense_force</option> 244 <option value="sense_force">sense_force</option>
235 <option value="antisense_filter">antisense_filter</option> 247 <option value="antisense_filter">antisense_filter</option>
236 </param> 248 </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)" > 249 <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" /> 250 <validator type="in_range" message="trimendexons must be positive" min="1" />
239 </param> 251 </param>
252 <param name="find_shifted_canonical" type="boolean" truevalue="--find-shifted-canonical-species" falsevalue="" checked="false" label="find-shifted-canonical Use a more sensitive search for canonical splicing" help=""/>
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"/> 253 <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"/>
241 254
242 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns"> 255 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns">
243 <option value="1">high reward (default)</option> 256 <option value="1">high reward (default)</option>
244 <option value="0">low reward</option> 257 <option value="0">low reward</option>
326 <option value="gff3_match_cdna">GFF3 match cDNA format</option> 339 <option value="gff3_match_cdna">GFF3 match cDNA format</option>
327 <option value="gff3_match_est">GFF3 match EST format</option> 340 <option value="gff3_match_est">GFF3 match EST format</option>
328 <option value="splicesites">splicesites output (for GSNAP)</option> 341 <option value="splicesites">splicesites output (for GSNAP)</option>
329 <option value="introns">introns output (for GSNAP)</option> 342 <option value="introns">introns output (for GSNAP)</option>
330 <option value="map_exons">IIT FASTA exon map format</option> 343 <option value="map_exons">IIT FASTA exon map format</option>
331 <option value="map_genes">IIT FASTA map format</option> 344 <option value="map_ranges">IIT FASTA map format</option>
332 <option value="coords">coords in table format</option> 345 <option value="coords">coords in table format</option>
333 <option value="sam" selected="true">SAM format</option> 346 <option value="sam" selected="true">SAM format</option>
334 </param> 347 </param>
335 <when value="gmap"> 348 <when value="gmap">
336 </when> 349 </when>
351 <when value="gff3_match_cdna"/> 364 <when value="gff3_match_cdna"/>
352 <when value="gff3_match_est"/> 365 <when value="gff3_match_est"/>
353 <when value="splicesites"/> 366 <when value="splicesites"/>
354 <when value="introns"/> 367 <when value="introns"/>
355 <when value="map_exons"/> 368 <when value="map_exons"/>
356 <when value="map_genes"/> 369 <when value="map_ranges"/>
357 <when value="coords"/> 370 <when value="coords"/>
358 <when value="sam"> 371 <when value="sam">
359 <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/> 372 <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 '@'"/> 373 <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 2011-11-30 374 <!-- Removed in gmap version 2011-11-30
367 --> 380 -->
368 <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/> 381 <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"/> 382 <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"/> 383 <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"/> 384 <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/>
385 <param name="sam_use_0M" type="boolean" truevalue="--sam-use-0M" falsevalue="" checked="false" label="Insert 0M in CIGAR between adjacent insertions and deletions" help="Required by Picard, but can cause errors in other tools"/>
386 <param name="force_xs_dir" type="boolean" truevalue="--force-xs-dir" falsevalue="" checked="false" label="Force direction (disallow XS:A:?)"
387 help="For RNA-Seq alignments, disallows XS:A:? when the sense direction is unclear, and replaces this value arbitrarily with XS:A:+. May be useful for some programs, such as Cufflinks, that cannot handle XS:A:?. However, if you use this flag, the reported value of XS:A:+ in these cases will not be meaningful."/>
388 <param name="md_lowercase_snp" type="boolean" truevalue="--md-lowercase-snp" falsevalue="" checked="false" label="MD lowercase SNP"
389 help="In MD string, when known SNPs are given by the -v flag, prints difference nucleotides as lower-case when they, differ from reference but match a known alternate allele"/>
372 </when> 390 </when>
373 </conditional> <!-- name="result" --> 391 </conditional> <!-- name="result" -->
374 392
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)"/> 393 <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)"/>
376 394
380 mapexons Map each exon separately 398 mapexons Map each exon separately
381 mapboth Report hits from both strands of genome 399 mapboth Report hits from both strands of genome
382 flanking=INT Show flanking hits (default 0) 400 flanking=INT Show flanking hits (default 0)
383 print-comment Show comment line for each hit 401 print-comment Show comment line for each hit
384 --> 402 -->
403
404 <!--
405 min-trimmed-coverage=FLOAT Do not print alignments with trimmed coverage less
406 this value (default=0.0, which means no filtering)
407 Note that chimeric alignments will be output regardless
408 of this filter
409 min-identity=FLOAT Do not print alignments with identity less
410 this value (default=0.0, which means no filtering)
411 Note that chimeric alignments will be output regardless
412 of this filter
413 -->
414
385 415
386 416
387 </inputs> 417 </inputs>
388 <outputs> 418 <outputs>
389 <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/> 419 <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/>