Mercurial > repos > jjohnson > gmap
annotate gsnap.xml @ 3:488e9d642566 draft
GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress
| author | peterjc |
|---|---|
| date | Wed, 28 Sep 2016 10:47:28 -0400 |
| parents | f6ba0f12cca2 |
| children | 14561eb803a5 |
| rev | line source |
|---|---|
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GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress
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1 <tool id="gsnap" name="GSNAP" version="3.0.1"> |
| 0 | 2 <description>Genomic Short-read Nucleotide Alignment Program</description> |
| 3 <requirements> | |
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4 <requirement type="package" version="2013-05-09">gmap</requirement> |
| 0 | 5 </requirements> |
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6 <version_command>gsnap --version</version_command> |
| 0 | 7 <command> |
| 8 #import os.path, re | |
| 9 gsnap | |
| 10 --nthreads="4" --ordered | |
| 11 #if $refGenomeSource.genomeSource == "gmapdb": | |
| 12 --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name | |
| 13 #else: | |
| 14 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) | |
| 15 #end if | |
| 16 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: | |
| 17 --kmer=$refGenomeSource.kmer | |
| 18 #end if | |
| 19 #if $refGenomeSource.use_splicing.src == 'gmapdb': | |
| 20 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: | |
| 21 -s $refGenomeSource.use_splicing.splicemap.value | |
| 22 #if $computation.trim_mismatch_score.__str__ == '0': | |
| 23 $ambig_splice_noclip | |
| 24 #end if | |
| 25 #end if | |
| 26 #elif $refGenomeSource.use_splicing.src == 'history': | |
| 27 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: | |
| 28 -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap) | |
| 29 #if $computation.trim_mismatch_score.__str__ == '0': | |
| 30 $ambig_splice_noclip | |
| 31 #end if | |
| 32 #end if | |
| 33 #end if | |
| 34 #if $refGenomeSource.use_snps.src == 'gmapdb': | |
| 35 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: | |
| 36 -v $refGenomeSource.use_snps.snpindex.value | |
| 37 #end if | |
| 38 #elif $refGenomeSource.use_snps.src == 'history': | |
| 39 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: | |
| 40 -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name | |
| 41 #end if | |
| 42 #end if | |
| 43 #if $refGenomeSource.mode.__str__ != '': | |
| 44 --mode=$refGenomeSource.mode | |
| 45 #end if | |
| 46 #* ## No longer in options as of version 2011-11-30 | |
| 47 #if $mapq_unique_score.__str__ != '': | |
| 48 --mapq-unique-score=$mapq_unique_score | |
| 49 #end if | |
| 50 *# | |
| 51 #if $computation.options == "advanced": | |
| 52 #if $computation.max_mismatches.__str__ != '': | |
| 53 --max-mismatches=$computation.max_mismatches | |
| 54 #end if | |
| 55 $computation.query_unk_mismatch | |
| 56 $computation.genome_unk_mismatch | |
| 57 #if $computation.terminal_threshold.__str__ != '': | |
| 58 --terminal-threshold=$computation.terminal_threshold | |
| 59 #end if | |
| 60 #if $computation.indel_penalty.__str__ != '': | |
| 61 --indel-penalty=$computation.indel_penalty | |
| 62 #end if | |
| 63 #if $computation.indel_endlength.__str__ != '': | |
| 64 --indel-endlength=$computation.indel_endlength | |
| 65 #end if | |
| 66 #if $computation.max_middle_insertions.__str__ != '': | |
| 67 --max-middle-insertions=$computation.max_middle_insertions | |
| 68 #end if | |
| 69 #if $computation.max_middle_deletions.__str__ != '': | |
| 70 --max-middle-deletions=$computation.max_middle_deletions | |
| 71 #end if | |
| 72 #if $computation.max_end_insertions.__str__ != '': | |
| 73 --max-end-insertions=$computation.max_end_insertions | |
| 74 #end if | |
| 75 #if $computation.max_end_deletions.__str__ != '': | |
| 76 --max-end-deletions=$computation.max_end_deletions | |
| 77 #end if | |
| 78 #if $computation.suboptimal_levels.__str__ != '': | |
| 79 --suboptimal-levels=$computation.suboptimal_levels | |
| 80 #end if | |
| 81 #if $computation.adapter_strip.__str__ != '': | |
| 82 --adapter-strip=$computation.adapter_strip | |
| 83 #end if | |
| 84 #if $computation.trim_mismatch_score.__str__ != '': | |
| 85 --trim-mismatch-score=$computation.trim_mismatch_score | |
| 86 #end if | |
| 87 #if $computation.trim_indel_score.__str__ != '': | |
| 88 --trim-indel-score=$computation.trim_indel_score | |
| 89 #end if | |
| 90 ## TODO - do we need these options (Is it tally XOR runlength?): | |
| 91 ## --tallydir= --use-tally=tally | |
| 92 ## --runlengthdir --use-runlength=runlength | |
| 93 #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0: | |
| 94 ##--tallydir $os.path.dirname($computation.use_tally) --use-tally $os.path.basename($computation.use_tally) | |
| 95 --use-tally=$computation.use_tally | |
| 96 #end if | |
| 97 ## gmap options | |
| 98 #if $computation.gmap_mode.__str__ != '' and $computation.gmap_mode.__str__ != 'None': | |
| 99 --gmap-mode='$computation.gmap_mode' | |
| 100 #end if | |
| 101 #if $computation.trigger_score_for_gmap.__str__ != '': | |
| 102 --trigger-score-for-gmap=$computation.trigger_score_for_gmap | |
| 103 #end if | |
| 104 #if $computation.max_gmap_pairsearch.__str__ != '' and $re.search("pairsearch",$computation.gmap_mode): | |
| 105 --max-gmap-pairsearch=$computation.max_gmap_pairsearch | |
| 106 #end if | |
| 107 #if $computation.max_gmap_terminal.__str__ != '' and $re.search("terminal",$computation.gmap_mode): | |
| 108 --max-gmap-terminal=$computation.max_gmap_terminal | |
| 109 #end if | |
| 110 #if $computation.max_gmap_improvement.__str__ != '' and $re.search("improv",$computation.gmap_mode): | |
| 111 --max-gmap-improvement=$computation.max_gmap_improvement | |
| 112 #end if | |
| 113 #if $computation.microexon_spliceprob.__str__ != '': | |
| 114 --microexon-spliceprob=$computation.microexon_spliceprob | |
| 115 #end if | |
| 116 #end if | |
| 117 #if $splicing.options == "advanced": | |
| 118 $splicing.novelsplicing | |
| 119 #if $splicing.localsplicedist.__str__ != '': | |
| 120 --localsplicedist=$splicing.localsplicedist | |
| 121 #end if | |
| 122 #if $splicing.local_splice_penalty.__str__ != '': | |
| 123 --local-splice-penalty=$splicing.local_splice_penalty | |
| 124 #end if | |
| 125 #if $splicing.distant_splice_penalty.__str__ != '': | |
| 126 --distant-splice-penalty=$splicing.distant_splice_penalty | |
| 127 #end if | |
| 128 #if $splicing.local_splice_endlength.__str__ != '': | |
| 129 --local-splice-endlength=$splicing.local_splice_endlength | |
| 130 #end if | |
| 131 #if $splicing.distant_splice_endlength.__str__ != '': | |
| 132 --distant-splice-endlength=$splicing.distant_splice_endlength | |
| 133 #end if | |
| 134 #if $splicing.distant_splice_identity.__str__ != '': | |
| 135 --distant-splice-identity=$splicing.distant_splice_identity | |
| 136 #end if | |
| 137 #end if | |
| 138 #if $output.options == "advanced": | |
| 139 #if $output.npath.__str__ != '': | |
| 140 --npath=$output.npath | |
| 141 #end if | |
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142 #if $output.maxsearch.__str__ != '': |
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143 --maxsearch=$output.maxsearch |
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144 #end if |
| 0 | 145 $output.quiet_if_excessive |
| 146 $output.show_refdiff | |
| 147 $output.clip_overlap | |
| 148 #end if | |
| 149 #if $result.format == "sam": | |
| 150 --format=sam | |
| 151 $result.no_sam_headers | |
| 152 #if $result.read_group_id.__str__.strip != '': | |
| 153 --read-group-id='$result.read_group_id' | |
| 154 #end if | |
| 155 #if $result.read_group_name.__str__ != '': | |
| 156 --read-group-name='$result.read_group_name' | |
| 157 #end if | |
| 158 #if $result.read_group_library.__str__ != '': | |
| 159 --read-group-library='$result.read_group_library' | |
| 160 #end if | |
| 161 #if $result.read_group_platform.__str__ != '': | |
| 162 --read-group-platform='$result.read_group_platform' | |
| 163 #end if | |
| 164 #if $result.quality_shift.__str__ != '': | |
| 165 --quality-shift=$result.quality_shift | |
| 166 #end if | |
| 167 #elif $result.format == "goby": | |
| 168 #if $result.goby_output.__str__ != '': | |
| 169 --goby-output='$result.goby_output' | |
| 170 #end if | |
| 171 #if $result.creads_window_start.__str__ != '': | |
| 172 --creads-window-start=$result.creads_window_start | |
| 173 #end if | |
| 174 #if $result.creads_window_end.__str__ != '': | |
| 175 --creads-window-end=$result.creads_window_end | |
| 176 #end if | |
| 177 $result.creads_complement | |
| 178 #end if | |
| 179 #if $results.split_output == 'yes': | |
| 180 --split-output=gsnap_out | |
| 181 #if $results.fails.choice == 'nofails': | |
| 182 --nofails | |
| 183 #elif $results.fails.choice == 'failsonly': | |
| 184 --failsonly | |
| 185 #end if | |
| 186 $results.fails_as_input | |
| 187 #else | |
| 188 #if $results.fails.choice == 'nofails': | |
| 189 --nofails | |
| 190 #elif $results.fails.choice == 'failsonly': | |
| 191 --failsonly | |
| 192 $results.fails.fails_as_input | |
| 193 #end if | |
| 194 #end if | |
| 195 #if $seq.format == "gsnap_fasta": | |
| 196 $seq.circularinput $seq.gsnap | |
| 197 #else if $seq.format == "fastq": | |
| 198 #if $seq.barcode_length.__str__ != '': | |
| 199 --barcode-length=$seq.barcode_length | |
| 200 #end if | |
| 201 #if $seq.fastq_id_start.__str__ != '': | |
| 202 --fastq-id-start=$seq.fastq_id_start | |
| 203 #end if | |
| 204 #if $seq.fastq_id_end.__str__ != '': | |
| 205 --fastq-id-end=$seq.fastq_id_end | |
| 206 #end if | |
| 207 #if $seq.filter_chastity.__str__ != 'off': | |
| 208 --filter-chastity=$seq.filter_chastity | |
| 209 #end if | |
| 210 #if $seq.paired.ispaired.__str__ == 'yes': | |
| 211 #if $seq.paired.pairmax_dna.__str__ != '': | |
| 212 --pairmax-dna=$seq.paired.pairmax_dna | |
| 213 #end if | |
| 214 #if $seq.paired.pairmax_rna.__str__ != '': | |
| 215 --pairmax-rna=$seq.paired.pairmax_rna | |
| 216 #end if | |
| 217 #if $seq.paired.pairexpect.__str__ != '': | |
| 218 --pairexpect=$seq.paired.pairexpect | |
| 219 #end if | |
| 220 #if $seq.paired.pairdev.__str__ != '': | |
| 221 --pairdev=$seq.paired.pairdev | |
| 222 #end if | |
| 223 $seq.fastq $seq.paired.fastq | |
| 224 #else | |
| 225 $seq.fastq | |
| 226 #end if | |
| 227 #end if | |
| 228 #if $results.split_output == 'yes': | |
| 229 2> $gsnap_stderr | |
| 230 #else: | |
| 231 #if $results.fails.choice.__str__ == 'failsonly' and $results.fails.fails_as_input.__str__ != '': | |
| 232 2> $gsnap_stderr > $gsnap_fq | |
| 233 #else | |
| 234 2> $gsnap_stderr > $gsnap_out | |
| 235 #end if | |
| 236 #end if | |
| 237 | |
| 238 </command> | |
| 239 <inputs> | |
| 240 <!-- Input data --> | |
| 241 <conditional name="seq"> | |
| 242 <param name="format" type="select" label="<H2>Input Sequences</H2>Select the input format" help=""> | |
| 243 <option value="fastq">Fastq</option> | |
| 244 <!-- | |
| 245 <option value="goby">Goby compact-reads</option> | |
| 246 --> | |
| 247 <option value="gsnap_fasta">GNSAP fasta</option> | |
| 248 </param> | |
| 249 <when value="fastq"> | |
| 250 <param name="fastq" type="data" format="fastq" label="Select a fastq dataset" /> | |
| 251 <conditional name="paired"> | |
| 252 <param name="ispaired" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use Paired Reads?"/> | |
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253 <when value="no"> |
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254 <!-- |
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255 Could allow multiple input fastq and set the force-single-end flag |
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256 force-single-end When multiple FASTQ files are provided on the command line, GSNAP assumes |
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257 they are match paired-end files. This flag treats each file as single-end. |
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258 --> |
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259 </when> |
| 0 | 260 <when value="yes"> |
| 261 <param name="fastq" type="data" format="fastq" label="Select the paired reads reverse dataset" /> | |
| 262 <param name="orientation" type="select" label="Orientation of paired-end reads" help=""> | |
| 263 <option value="FR">fwd-rev, typical Illumina default</option> | |
| 264 <option value="RF">rev-fwd, for circularized inserts</option> | |
| 265 <option value="FF">fwd-fwd, same strand</option> | |
| 266 </param> | |
| 267 <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."/> | |
| 268 <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."/> | |
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269 <param name="pairexpect" type="integer" value="" optional="true" label="Expected paired-end length" |
| 0 | 270 help="Used for calling splices in medial part of paired-end reads (default 200)"/> |
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271 <param name="pairdev" type="integer" value="" optional="true" label="Allowable deviation from expected paired-end length" |
| 0 | 272 help="Used for calling splices in medial part of paired-end reads (default 25)"/> |
| 273 </when> | |
| 274 </conditional> | |
| 275 <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" /> | |
| 276 <param name="fastq_id_start" type="integer" value="" optional="true" label="Starting field of identifier in FASTQ header, whitespace-delimited, starting from 1" /> | |
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277 <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, whitespace-delimited, starting from 1" |
| 0 | 278 help="Examples: |
| 279 <br>@HWUSI-EAS100R:6:73:941:1973#0/1 | |
| 280 <br> . start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0/1 | |
| 281 <br>@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 | |
| 282 <br> . start=1, end=1 => identifier is SRR001666.1 | |
| 283 <br> . start=2, end=2 => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345 | |
| 284 <br> . start=1, end=2 => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345" | |
| 285 /> | |
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286 <param name="filter_chastity" type="select" label="Skip reads marked by the Illumina chastity program" |
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287 help="String after the accession having a 'Y' after the first colon, like this: |
| 0 | 288 <br>@accession 1:Y:0:CTTGTA |
| 289 <br>where the 'Y' signifies filtering by chastity. | |
| 290 <br> For 'either', a 'Y' on either end of a paired-end read will be filtered. | |
| 291 <br> For 'both', a 'Y' is required on both ends of a paired-end read (or on the only end of a single-end read)" | |
| 292 > | |
| 293 <option value="off">off - no filtering</option> | |
| 294 <option value="either">either - a 'Y' on either end of a paired-end read</option> | |
| 295 <option value="both">both - a 'Y' is required on both ends of a paired-end read or the only end of a single-end read</option> | |
| 296 </param> | |
| 297 </when> | |
| 298 <!-- | |
| 299 <when value="goby"> | |
| 300 </when> | |
| 301 --> | |
| 302 <when value="gsnap_fasta"> | |
| 303 <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"/> | |
| 304 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/> | |
| 305 </when> | |
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306 |
| 0 | 307 </conditional> |
| 308 <!-- No longer in options as of version 2011-11-30 | |
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309 <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold" |
| 0 | 310 help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this |
| 311 (if not selected, then reports all multiple results, up to npaths)" /> | |
| 312 --> | |
| 313 | |
| 314 <!-- GMAPDB for alignment --> | |
| 315 <conditional name="refGenomeSource"> | |
| 316 <param name="genomeSource" type="select" label="<HR><H2>Align To</H2>Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> | |
| 317 <option value="indexed">Use a built-in index</option> | |
| 318 <option value="gmapdb">Use a gmapdb from your history</option> | |
| 319 </param> | |
| 320 <when value="indexed"> | |
| 321 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> | |
| 322 <options from_file="gmap_indices.loc"> | |
| 323 <column name="uid" index="0" /> | |
| 324 <column name="dbkey" index="1" /> | |
| 325 <column name="name" index="2" /> | |
| 326 <column name="kmers" index="3" /> | |
| 327 <column name="maps" index="4" /> | |
| 328 <column name="snps" index="5" /> | |
| 329 <column name="value" index="6" /> | |
| 330 </options> | |
| 331 </param> | |
| 332 | |
| 333 <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> | |
| 334 <options from_file="gmap_indices.loc"> | |
| 335 <column name="name" index="3"/> | |
| 336 <column name="value" index="3"/> | |
| 337 <filter type="param_value" ref="gmapindex" column="6"/> | |
| 338 <filter type="multiple_splitter" column="3" separator=","/> | |
| 339 <filter type="add_value" name="" value=""/> | |
| 340 <filter type="sort_by" column="3"/> | |
| 341 </options> | |
| 342 </param> | |
| 343 | |
| 344 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase."> | |
| 345 <option value="">standard</option> | |
| 346 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> | |
| 347 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> | |
| 348 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option> | |
| 349 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option> | |
| 350 </param> | |
| 351 | |
| 352 <conditional name="use_splicing"> | |
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353 <param name="src" type="select" label="<HR>Known Splicesite and Introns" |
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354 help="Look for splicing involving known sites or known introns at short or long distances |
| 0 | 355 See README instructions for the distinction between known sites and known introns"> |
| 356 <option value="none" selected="true">None</option> | |
| 357 <option value="gmapdb">From the GMAP Database</option> | |
| 358 <option value="history">A Map in your history</option> | |
| 359 </param> | |
| 360 <when value="none"/> | |
| 361 <when value="history"> | |
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362 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" label="Select a splicesite map" |
| 0 | 363 help="built with GMAP IIT"/> |
| 364 </when> | |
| 365 <when value="gmapdb"> | |
| 366 <param name="splicemap" type="select" data_ref="gmapindex" label="Use map for splicing involving known sites or known introns" help=""> | |
| 367 <options from_file="gmap_indices.loc"> | |
| 368 <column name="name" index="4"/> | |
| 369 <column name="value" index="4"/> | |
| 370 <filter type="param_value" ref="gmapindex" column="6"/> | |
| 371 <filter type="multiple_splitter" column="4" separator=","/> | |
| 372 <filter type="add_value" name="" value=""/> | |
| 373 <filter type="sort_by" column="4"/> | |
| 374 </options> | |
| 375 </param> | |
| 376 </when> | |
| 377 </conditional> | |
| 378 | |
| 379 <conditional name="use_snps"> | |
| 380 <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments"> | |
| 381 <option value="none" selected="true">None</option> | |
| 382 <option value="gmapdb">From the GMAP Database</option> | |
| 383 <option value="history">A SNP Index in your history</option> | |
| 384 </param> | |
| 385 <when value="none"/> | |
| 386 <when value="history"> | |
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387 <param name="snpindex" type="data" format="gmapsnpindex" label="Select a snpindex" |
| 0 | 388 help="built with GMAP SNP Index"/> |
| 389 </when> | |
| 390 <when value="gmapdb"> | |
| 391 <param name="snpindex" type="select" data_ref="gmapindex" label="Use database containing known SNPs" help=""> | |
| 392 <options from_file="gmap_indices.loc"> | |
| 393 <column name="name" index="5"/> | |
| 394 <column name="value" index="5"/> | |
| 395 <filter type="param_value" ref="gmapindex" column="6"/> | |
| 396 <filter type="multiple_splitter" column="5" separator=","/> | |
| 397 <filter type="add_value" name="" value=""/> | |
| 398 <filter type="sort_by" column="5"/> | |
| 399 </options> | |
| 400 </param> | |
| 401 </when> | |
| 402 </conditional> | |
| 403 | |
| 404 </when> | |
| 405 <when value="gmapdb"> | |
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406 <param name="gmapdb" type="data" format="gmapdb" label="Select a gmapdb" |
| 0 | 407 help="A GMAP database built with GMAP Build"/> |
| 408 <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> | |
| 409 <options> | |
| 410 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> | |
| 411 </options> | |
| 412 </param> | |
| 413 | |
| 414 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase."> | |
| 415 <option value="">standard</option> | |
| 416 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> | |
| 417 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> | |
| 418 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option> | |
| 419 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option> | |
| 420 </param> | |
| 421 | |
| 422 <conditional name="use_splicing"> | |
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423 <param name="src" type="select" label="<HR>Known Splicesite and Introns" |
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424 help="Look for splicing involving known sites or known introns at short or long distances |
| 0 | 425 See README instructions for the distinction between known sites and known introns"> |
| 426 <option value="none" selected="true">None</option> | |
| 427 <option value="gmapdb">From the GMAP Database</option> | |
| 428 <option value="history">A Map in your history</option> | |
| 429 </param> | |
| 430 <when value="none"/> | |
| 431 <when value="history"> | |
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432 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" label="Select a splicesite map" |
| 0 | 433 help="built with GMAP IIT"/> |
| 434 <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites" | |
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435 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. |
| 0 | 436 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/> |
| 437 </when> | |
| 438 <when value="gmapdb"> | |
| 439 <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> | |
| 440 <options> | |
| 441 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> | |
| 442 </options> | |
| 443 </param> | |
| 444 <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites" | |
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445 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. |
| 0 | 446 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/> |
| 447 </when> | |
| 448 </conditional> | |
| 449 | |
| 450 <conditional name="use_snps"> | |
| 451 <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments"> | |
| 452 <option value="none" selected="true">None</option> | |
| 453 <option value="gmapdb">From the GMAP Database</option> | |
| 454 <option value="history">A SNP Index in your history</option> | |
| 455 </param> | |
| 456 <when value="none"/> | |
| 457 <when value="history"> | |
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458 <param name="snpindex" type="data" format="gmapsnpindex" label="Select a snpindex" |
| 0 | 459 help="built with GMAP SNP Index"/> |
| 460 </when> | |
| 461 <when value="gmapdb"> | |
| 462 <param name="snpindex" type="select" data_ref="gmapdb" label="Use database containing known SNPs" help=""> | |
| 463 <options> | |
| 464 <filter type="data_meta" ref="gmapdb" key="snps" multiple="True" separator=","/> | |
| 465 </options> | |
| 466 </param> | |
| 467 </when> | |
| 468 </conditional> | |
| 469 | |
| 470 </when> | |
| 471 </conditional> | |
| 472 | |
| 473 <!-- Computation options --> | |
| 474 <conditional name="computation"> | |
| 475 <param name="options" type="select" label="<HR>Computational Settings" help=""> | |
| 476 <option value="default">Use default settings</option> | |
| 477 <option value="advanced">Set Computation Options</option> | |
| 478 </param> | |
| 479 <when value="default"/> | |
| 480 <when value="advanced"> | |
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481 <param name="max_mismatches" type="float" value="" optional="true" label="Maximum number of mismatches allowed (uses default when negative)" |
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482 help="Maximum number of mismatches allowed (if not specified, then |
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483 defaults to the ultrafast level of ((readlength+index_interval-1)/kmer - 2)) |
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484 (By default, the genome index interval is 3, but this can be changed |
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485 by providing a different value for -q to gmap_build when processing the genome.) |
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486 If specified between 0.0 and 1.0, then treated as a fraction |
| 0 | 487 of each read length. Otherwise, treated as an integral number |
| 488 of mismatches (including indel and splicing penalties) | |
| 489 For RNA-Seq, you may need to increase this value slightly | |
| 490 to align reads extending past the ends of an exon."> | |
| 491 <validator type="in_range" message="The mismatches must >= 0." min="0."/> | |
| 492 </param> | |
| 493 <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"/> | |
| 494 <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"/> | |
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495 <param name="maxsearch" type="integer" value="" optional="true" label="Maximum number of alignments to find (default 1000)" |
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496 help="Must be larger than paths, which is the number to report. |
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497 Keeping this number large will allow for random selection among multiple alignments. |
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498 Reducing this number can speed up the program. "/> |
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499 |
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500 <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment" |
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501 help="Threshold for searching for a terminal alignment (from one end of the |
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502 read to the best possible position at the other end) (default 2 |
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503 for standard, atoi-stranded, and atoi-nonstranded mode; default 100 |
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504 for cmet-stranded and cmet-nonstranded mode). |
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505 For example, if this value is 2, then if GSNAP finds an exact or |
| 0 | 506 1-mismatch alignment, it will not try to find a terminal alignment. |
| 507 Note that this default value may not be low enough if you want to | |
| 508 obtain terminal alignments for very short reads, although such reads | |
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509 probably don't have enough specificity for terminal alignments anyway. |
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510 To turn off terminal alignments, set this to a high value, greater |
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511 than the value for max-mismatches. |
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512 "/> |
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513 <param name="indel_penalty" type="integer" value="" optional="true" label="Penalty for an indel (default 2)" |
| 0 | 514 help="Counts against mismatches allowed. To find indels, make indel-penalty less than or equal to max-mismatches. A value < 2 can lead to false positives at read ends" /> |
| 515 <param name="indel_endlength" type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" /> | |
| 516 <param name="max_middle_insertions" type="integer" value="" optional="true" label="Maximum number of middle insertions allowed (default 9)" /> | |
| 517 <param name="max_middle_deletions" type="integer" value="" optional="true" label="Maximum number of middle deletions allowed (default 30)" /> | |
| 518 <param name="max_end_insertions" type="integer" value="" optional="true" label="Maximum number of end insertions allowed (default 3)" /> | |
| 519 <param name="max_end_deletions" type="integer" value="" optional="true" label="Maximum number of end deletions allowed (default 6)" /> | |
| 520 <param name="suboptimal_levels" type="integer" value="" optional="true" label="Report suboptimal hits beyond best hit (default 0)" | |
| 521 help="All hits with best score plus suboptimal-levels are reported" /> | |
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522 <param name="adapter_strip" type="select" label="Method for removing adapters from reads" |
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523 help="Default is 'off'. To turn on, specify 'paired', which removes adapters |
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524 from paired-end reads if they appear to be present."> |
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525 <option value="paired">paired</option> |
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526 <option value="off" selected="true">off</option> |
| 0 | 527 </param> |
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528 <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)" |
| 0 | 529 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/> |
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530 <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)" |
| 0 | 531 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/> |
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532 <param name="use_tally" type="data" format="tally.iit" optional="true" label="Select a tally IIT file to resolve concordant multiple results" |
| 0 | 533 help="generated by gsnap_tally and iit_store"/> |
| 534 | |
| 535 <!-- | |
| 536 tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is | |
| 537 location of genome index files specified using -D and -d). Note: can | |
| 538 just give full path name to use-tally instead. | |
| 539 use-tally=STRING Use this tally IIT file to resolve concordant multiple results | |
| 540 runlengthdir=STRING Directory for runlength IIT file to resolve concordant multiple results (default is | |
| 541 location of genome index files specified using -D and -d). Note: can | |
| 542 just give full path name to use-runlength instead. | |
| 543 use-runlength=STRING Use this runlength IIT file to resolve concordant multiple results | |
| 544 --> | |
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545 |
| 0 | 546 <!-- Options for GMAP alignment within GSNAP --> |
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547 <param name="gmap_mode" type="select" multiple="true" optional="true" display="checkboxes" label="Cases to use GMAP for complex alignments containing multiple splices or indels" |
| 0 | 548 help="Default: pairsearch,terminal,improve"> |
| 549 <option value="pairsearch" selected="true">pairsearch</option> | |
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550 <option value="indel_knownsplice" selected="true">indel_knownsplice</option> |
| 0 | 551 <option value="terminal" selected="true">terminal</option> |
| 552 <option value="improve" selected="true">improve</option> | |
| 553 </param> | |
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554 <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)" |
| 0 | 555 help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" /> |
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556 <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)" |
| 0 | 557 help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." /> |
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558 <param name="max_gmap_terminal" type="integer" value="" optional="true" label="GMAP terminal threshold (default 3)" |
| 0 | 559 help="Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 3)." /> |
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560 <param name="max_gmap_improvement" type="integer" value="" optional="true" label="GMAP improvement threshold (default 3)" |
| 0 | 561 help="Perform GMAP improvement on nearby genomic regions up to this many candidate ends (default 3)." /> |
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562 <param name="microexon_spliceprob" type="float" value="" optional="true" label="GMAP microexons threshold (default .90)" |
| 0 | 563 help="Allow microexons only if one of the splice site probabilities is greater than this value." > |
| 564 <validator type="in_range" message="The microexons probability must be between 0. and 1." min="0." max="1."/> | |
| 565 </param> | |
| 566 </when> | |
| 567 </conditional> | |
| 568 | |
| 569 <conditional name="splicing"> | |
| 570 <param name="options" type="select" label="<HR>Splicing options for RNA-Seq" help=""> | |
| 571 <option value="default">Use default settings</option> | |
| 572 <option value="advanced">Set Splicing Options</option> | |
| 573 </param> | |
| 574 <when value="default"/> | |
| 575 <when value="advanced"> | |
| 576 <!-- Splicing options for RNA-Seq --> | |
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577 <!-- use-splicing This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splicing --> |
| 0 | 578 <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) --> |
| 579 <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/> | |
| 580 <param name="localsplicedist" type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/> | |
| 581 <param name="local_splice_penalty" type="integer" value="" optional="true" label="Penalty for a local splice (default 0). Counts against mismatches allowed"/> | |
| 582 <param name="distant_splice_penalty" type="integer" value="" optional="true" label="Penalty for a distant splice (default 3). Counts against mismatches allowed" | |
| 583 help="A distant splice is one where the intron length exceeds the value of localsplicedist or is an | |
| 584 inversion, scramble, or translocation between two different chromosomes. Counts against mismatches allowed"/> | |
| 585 <param name="distant_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments" | |
| 586 help="(default 16, min is the kmer length)"/> | |
| 587 <param name="shortend_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for short-end spliced alignments" | |
| 588 help="(default 2, but unless known splice sites are provided, GSNAP may still need the end length to be the value of kmer size to find a given splice"/> | |
| 589 <param name="distant_splice_identity" type="float" value="" optional="true" label="Minimum identity at end required for distant spliced alignments (default 0.95)"/> | |
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590 <param name="antistranded_penalty" type="integer" value="" optional="true" label="Penalty for antistranded splicing when using stranded RNA-Seq protocols" |
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591 help="A positive value, such as 1, expects antisense on the first read and sense on the second read. |
| 0 | 592 Default is 0, which treats sense and antisense equally well"/> |
| 593 </when> | |
| 594 </conditional> | |
| 595 | |
| 596 <!-- Output data --> | |
| 597 <conditional name="output"> | |
| 598 <param name="options" type="select" label="<HR><H2>Output</H2>Output options for RNA-Seq" help=""> | |
| 599 <option value="default">Use default settings</option> | |
| 600 <option value="advanced">Set Output Options</option> | |
| 601 </param> | |
| 602 <when value="default"/> | |
| 603 <when value="advanced"> | |
| 604 <param name="npath" type="integer" value="" optional="true" label="Maximum number of paths to print (default 100)"/> | |
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605 <param name="quiet_if_excessive" type="boolean" checked="false" truevalue="--quiet-if-excessive" falsevalue="" label="Quiet if Excessive" |
| 0 | 606 help="If more than maximum number of paths are found, then nothing is printed."/> |
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607 <param name="show_refdiff" type="boolean" checked="false" truevalue="--show-refdiff" falsevalue="" label="Show SNP-tolerant alignment" |
| 0 | 608 help="For GSNAP output in SNP-tolerant alignment, shows all differences relative to the reference genome as lower case (otherwise, it shows all differences relative to both the reference and alternate genome)"/> |
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609 <param name="clip_overlap" type="boolean" checked="false" truevalue="--clip-overlap" falsevalue="" label="Clip Overlap" |
| 0 | 610 help="For paired-end reads whose alignments overlap, clip the overlapping region."/> |
| 611 </when> | |
| 612 </conditional> | |
| 613 <conditional name="result"> | |
| 614 <param name="format" type="select" label="Select the output format" help=""> | |
| 615 <option value="sam">SAM</option> | |
| 616 <!-- goby should only be an option if the input is in goby format | |
| 617 <option value="goby">Goby</option> | |
| 618 --> | |
| 619 <option value="gsnap">GSNAP default output</option> | |
| 620 </param> | |
| 621 <when value="gsnap"> | |
| 622 </when> | |
| 623 <when value="sam"> | |
| 624 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> | |
| 625 <param name="read_group_id" type="text" value="" optional="true" label="Value to put into read-group id (RG-ID) field"/> | |
| 626 <param name="read_group_name" type="text" value="" optional="true" label="Value to put into read-group name (RG-SM) field"/> | |
| 627 <param name="read_group_library" type="text" value="" optional="true" label="Value to put into read-group library (RG-LB) field"/> | |
| 628 <param name="read_group_platform" type="text" value="" optional="true" label="Value to put into read-group library platform (RG-PL) field"/> | |
| 629 <param name="quality_shift" type="integer" value="" optional="true" label="Shift FASTQ quality scores by this amount in SAM output (default -31)"/> | |
| 630 </when> | |
| 631 <!-- | |
| 632 <when value="goby"> | |
| 633 <param name="goby_output" type="text" value="" label="Basename for Goby output files"/> | |
| 634 <param name="creads_window_start" type="integer" value="" optional="true" label="Compact reads window start (default: 0=start of file)"/> | |
| 635 <param name="creads_window_end" type="integer" value="" optional="true" label="Compact reads window end (default: 0=end of file)"/> | |
| 636 <param name="creads_complement" type="boolean" truevalue="-\-creads-complement" falsevalue="" checked="false" label="Complement read sequences (without reversing)"/> | |
| 637 </when> | |
| 638 --> | |
| 639 </conditional> | |
| 640 <!-- TODO combine fails and split_output --> | |
| 641 | |
| 642 <conditional name="results"> | |
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643 <param name="split_output" type="select" label="<HR>Split outputs" |
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644 help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results"> |
| 0 | 645 <option value="no">no</option> |
| 646 <option value="yes">yes</option> | |
| 647 </param> | |
| 648 <when value="no"> | |
| 649 <conditional name="fails"> | |
| 650 <param name="choice" type="select" label="How to deal with fails" help=""> | |
| 651 <option value="default">default - include them in results</option> | |
| 652 <option value="nofails">nofails - exclude fails from results</option> | |
| 653 <option value="failsonly">failsonly - only output failing results</option> | |
| 654 </param> | |
| 655 <when value="default"/> | |
| 656 <when value="nofails"/> | |
| 657 <when value="failsonly"> | |
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658 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format" |
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659 help=""/> |
| 0 | 660 </when> |
| 661 </conditional> | |
| 662 </when> | |
| 663 <when value="yes"> | |
| 664 <conditional name="fails"> | |
| 665 <param name="choice" type="select" label="How to deal with fails" help=""> | |
| 666 <option value="default">default - include them in results</option> | |
| 667 <option value="nofails">nofails - exclude fails from results</option> | |
| 668 <option value="failsonly">failsonly - only output failing results</option> | |
| 669 </param> | |
| 670 <when value="default"/> | |
| 671 <when value="nofails"/> | |
| 672 <when value="failsonly"/> | |
| 673 </conditional> | |
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674 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format" |
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675 help=""/> |
| 0 | 676 </when> |
| 677 </conditional> | |
| 678 | |
| 679 </inputs> | |
| 680 <outputs> | |
| 681 <data format="txt" name="gsnap_stderr" label="${tool.name} on ${on_string}: gsnap.log"/> | |
| 682 | |
| 683 <data format="txt" name="gsnap_out" label="${tool.name} on ${on_string} ${result.format}" > | |
| 684 <filter>(results['split_output'] == 'no' and (results['fails']['choice'] != 'failsonly' or results['fails']['fails_as_input'] == False))</filter> | |
| 685 <change_format> | |
| 686 <when input="result['format']" value="sam" format="sam"/> | |
| 687 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 688 </change_format> | |
| 689 </data> | |
| 690 | |
| 691 <data format="fastq" name="gsnap_fq" label="${tool.name} on ${on_string} fails.fq" > | |
| 692 <filter>(results['split_output'] == 'no' and results['fails']['choice'] == 'failsonly' and results['fails']['fails_as_input'] == True)</filter> | |
| 693 </data> | |
| 694 | |
| 695 <!-- nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, concordant_mult --> | |
| 696 | |
| 697 <data format="txt" name="unpaired_mult" label="${tool.name} on ${on_string} unpaired_mult.${result.format}" from_work_dir="gsnap_out.unpaired_mult"> | |
| 698 <filter>(results['split_output'] == 'yes')</filter> | |
| 699 <change_format> | |
| 700 <when input="result['format']" value="sam" format="sam"/> | |
| 701 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 702 </change_format> | |
| 703 </data> | |
| 704 <data format="txt" name="unpaired_uniq" label="${tool.name} on ${on_string} unpaired_uniq.${result.format}" from_work_dir="gsnap_out.unpaired_uniq"> | |
| 705 <filter>(results['split_output'] == 'yes')</filter> | |
| 706 <change_format> | |
| 707 <when input="result['format']" value="sam" format="sam"/> | |
| 708 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 709 </change_format> | |
| 710 </data> | |
| 711 <data format="txt" name="unpaired_transloc" label="${tool.name} on ${on_string} unpaired_transloc.${result.format}" from_work_dir="gsnap_out.unpaired_transloc"> | |
| 712 <filter>(results['split_output'] == 'yes')</filter> | |
| 713 <change_format> | |
| 714 <when input="result['format']" value="sam" format="sam"/> | |
| 715 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 716 </change_format> | |
| 717 </data> | |
| 718 <data format="txt" name="halfmapping_mult" label="${tool.name} on ${on_string} halfmapping_mult.${result.format}" from_work_dir="gsnap_out.halfmapping_mult"> | |
| 719 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 720 <change_format> | |
| 721 <when input="result['format']" value="sam" format="sam"/> | |
| 722 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 723 </change_format> | |
| 724 </data> | |
| 725 <data format="txt" name="halfmapping_uniq" label="${tool.name} on ${on_string} halfmapping_uniq.${result.format}" from_work_dir="gsnap_out.halfmapping_uniq"> | |
| 726 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 727 <change_format> | |
| 728 <when input="result['format']" value="sam" format="sam"/> | |
| 729 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 730 </change_format> | |
| 731 </data> | |
| 732 <data format="txt" name="halfmapping_transloc" label="${tool.name} on ${on_string} halfmapping_transloc.${result.format}" from_work_dir="gsnap_out.halfmapping_transloc"> | |
| 733 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 734 <change_format> | |
| 735 <when input="result['format']" value="sam" format="sam"/> | |
| 736 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 737 </change_format> | |
| 738 </data> | |
| 739 <data format="txt" name="paired_mult" label="${tool.name} on ${on_string} paired_mult.${result.format}" from_work_dir="gsnap_out.paired_mult"> | |
| 740 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 741 <change_format> | |
| 742 <when input="result['format']" value="sam" format="sam"/> | |
| 743 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 744 </change_format> | |
| 745 </data> | |
| 746 <data format="txt" name="paired_uniq" label="${tool.name} on ${on_string} paired_uniq.${result.format}" from_work_dir="gsnap_out.paired_uniq"> | |
| 747 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 748 <change_format> | |
| 749 <when input="result['format']" value="sam" format="sam"/> | |
| 750 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 751 </change_format> | |
| 752 </data> | |
| 753 <data format="txt" name="paired_transloc" label="${tool.name} on ${on_string} paired_transloc.${result.format}" from_work_dir="gsnap_out.paired_transloc"> | |
| 754 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 755 <change_format> | |
| 756 <when input="result['format']" value="sam" format="sam"/> | |
| 757 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 758 </change_format> | |
| 759 </data> | |
| 760 | |
| 761 <data format="txt" name="concordant_mult" label="${tool.name} on ${on_string} concordant_mult.${result.format}" from_work_dir="gsnap_out.concordant_mult"> | |
| 762 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 763 <change_format> | |
| 764 <when input="result['format']" value="sam" format="sam"/> | |
| 765 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 766 </change_format> | |
| 767 </data> | |
| 768 <data format="txt" name="concordant_uniq" label="${tool.name} on ${on_string} concordant_uniq.${result.format}" from_work_dir="gsnap_out.concordant_uniq"> | |
| 769 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 770 <change_format> | |
| 771 <when input="result['format']" value="sam" format="sam"/> | |
| 772 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 773 </change_format> | |
| 774 </data> | |
| 775 <data format="txt" name="concordant_transloc" label="${tool.name} on ${on_string} concordant_transloc.${result.format}" from_work_dir="gsnap_out.concordant_transloc"> | |
| 776 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 777 <change_format> | |
| 778 <when input="result['format']" value="sam" format="sam"/> | |
| 779 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 780 </change_format> | |
| 781 </data> | |
| 782 | |
| 783 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gsnap_out.nomapping"> | |
| 784 <filter>(results['split_output'] == 'yes' and results['fails_as_input'] == False)</filter> | |
| 785 <change_format> | |
| 786 <when input="result['format']" value="sam" format="sam"/> | |
| 787 <when input="result['format']" value="gsnap" format="gsnap"/> | |
| 788 </change_format> | |
| 789 </data> | |
| 790 | |
| 791 <data format="fastq" name="nomapping_fq" label="${tool.name} on ${on_string} nomapping.fq" from_work_dir="gsnap_out.nomapping.fq"> | |
| 792 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == False)</filter> | |
| 793 </data> | |
| 794 | |
| 795 <data format="fastq" name="nomapping_1_fq" label="${tool.name} on ${on_string} nomapping.1.fq" from_work_dir="gsnap_out.nomapping.1.fq"> | |
| 796 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 797 </data> | |
| 798 | |
| 799 <data format="fastq" name="nomapping_2_fq" label="${tool.name} on ${on_string} nomapping.2.fq" from_work_dir="gsnap_out.nomapping.2.fq"> | |
| 800 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> | |
| 801 </data> | |
| 802 | |
| 803 <!-- Will problay need wrapper code to generate composite datatype for goby alignment | |
| 804 <data format="gobyalignment" name="goby_alignment" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.nomapping"> | |
| 805 <filter>result['format'] == 'goby'</filter> | |
| 806 </data> | |
| 807 --> | |
| 808 | |
| 809 </outputs> | |
| 810 <tests> | |
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811 </tests> |
| 0 | 812 |
| 813 <help> | |
| 814 | |
| 815 **What it does** | |
| 816 | |
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817 GSNAP_ (Genomic Short-read Nucleotide Alignment Program) is a short read aligner which can align both single- and paired-end reads as short as 14nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. It is developed by Thomas D. Wu of Genentech, Inc. |
| 0 | 818 Publication_ citation: Thomas D. Wu, Serban Nacu "Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010 Apr 1;26(7):873-81. Epub 2010 Feb 10. |
| 819 | |
| 820 .. _GSNAP: http://research-pub.gene.com/gmap/ | |
| 821 .. _Publication: http://bioinformatics.oupjournals.org/cgi/content/full/26/7/873 | |
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822 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed |
| 0 | 823 |
| 824 ------ | |
| 825 | |
| 826 **Know what you are doing** | |
| 827 | |
| 828 .. class:: warningmark | |
| 829 | |
| 830 You will want to read the README_ | |
| 831 | |
| 832 .. _README: http://research-pub.gene.com/gmap/src/README | |
| 833 | |
| 834 ------ | |
| 835 | |
| 836 **Input formats** | |
| 837 | |
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838 Input to GSNAP should be either in FASTQ or FASTA format. |
| 0 | 839 |
| 840 The FASTQ input may include quality scores, which will then be included in SAM | |
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841 output, if that output format is selected. |
| 0 | 842 |
| 843 For FASTA format, you should include one line per read (or end of a | |
| 844 paired-end read). The same FASTA file can have a mixture of | |
| 845 single-end and paired-end reads of varying lengths, if desired. | |
| 846 | |
| 847 Single-end reads: | |
| 848 | |
| 849 Each FASTA entry should contain one short read per line, like this | |
| 850 | |
| 851 >Header information | |
| 852 AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA | |
| 853 | |
| 854 Each short read can have a different length. However, the entire read | |
| 855 needs to be on a single line, and may not wrap around multiple lines. | |
| 856 If it extends to a second line, GSNAP will think that the read is | |
| 857 paired-end. | |
| 858 | |
| 859 | |
| 860 Paired-end reads: | |
| 861 | |
| 862 Each FASTA entry should contain two short reads, one per line, like | |
| 863 this | |
| 864 | |
| 865 >Header information | |
| 866 AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA | |
| 867 GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG | |
| 868 | |
| 869 By default, the program assumes that the second end is in the reverse | |
| 870 complement direction compared with the first end. If they are in the | |
| 871 same direction, you may need to use the --circular-input (or -c) flag. | |
| 872 | |
| 873 ( The Galaxy tool: "FASTA Width formatter" can be used to reformat fasta files to have single line sequences. ) | |
| 874 | |
| 875 ------ | |
| 876 | |
| 877 **Output formats in GSNAP** | |
| 878 | |
| 879 SAM output format | |
| 880 | |
| 881 Default GSNAP format | |
| 882 See the README_ | |
| 883 </help> | |
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884 <citations> |
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885 <citation type="doi">10.1093/bioinformatics/btq057</citation> |
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886 </citations> |
| 0 | 887 </tool> |
| 888 |