Mercurial > repos > jjohnson > gmap
annotate gmap/gsnap.xml @ 4:f49f5a460c74
GSNAP - add and refine param options for gmap v 2011-10-16
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 08 Nov 2011 13:02:32 -0600 |
| parents | 52da588232b0 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gsnap" name="GSNAP" version="2.0.0"> |
| 2 <description>Genomic Short-read Nucleotide Alignment Program</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">gsnap</requirement> | |
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5 <!-- proposed tag for added datatype dependencies --> |
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52da588232b0
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6 <requirement type="datatype">gmapdb</requirement> |
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7 <requirement type="datatype">gmapsnpindex</requirement> |
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8 <requirement type="datatype">splicesites.iit</requirement> |
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9 <requirement type="datatype">introns.iit</requirement> |
| 0 | 10 </requirements> |
| 11 <version_string>gsnap --version</version_string> | |
| 12 <command> | |
| 13 #import os.path, re | |
| 14 gsnap | |
| 15 --nthreads="4" --ordered | |
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16 #if $refGenomeSource.genomeSource == "gmapdb": |
| 0 | 17 #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0] |
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18 --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name |
| 0 | 19 #else: |
| 20 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) | |
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21 #end if |
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22 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: |
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23 --kmer=$refGenomeSource.kmer |
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24 #end if |
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25 #if $refGenomeSource.use_splicing.src == 'gmapdb': |
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26 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: |
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27 -s $refGenomeSource.use_splicing.splicemap.value |
| 0 | 28 #end if |
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29 #elif $refGenomeSource.use_splicing.src == 'history': |
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30 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: |
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31 -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap) |
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32 #end if |
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33 #end if |
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34 #if $refGenomeSource.use_snps.src == 'gmapdb': |
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35 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: |
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36 -v $refGenomeSource.use_snps.snpindex.value |
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37 #end if |
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38 #elif $refGenomeSource.use_snps.src == 'history': |
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39 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: |
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40 -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name |
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41 #end if |
| 0 | 42 #end if |
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43 #if $refGenomeSource.mode.__str__ != '': |
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44 --mode=$refGenomeSource.mode |
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45 #end if |
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46 #if $mapq_unique_score.__str__ != '': |
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47 --mapq-unique-score=$mapq_unique_score |
| 0 | 48 #end if |
| 49 #if $computation.options == "advanced": | |
| 50 #if $computation.max_mismatches.__str__ != '': | |
| 51 --max-mismatches=$computation.max_mismatches | |
| 52 #end if | |
| 53 $computation.query_unk_mismatch | |
| 54 $computation.genome_unk_mismatch | |
| 55 #if $computation.terminal_threshold.__str__ != '': | |
| 56 --terminal-threshold=$computation.terminal_threshold | |
| 57 #end if | |
| 58 #if $computation.indel_penalty.__str__ != '': | |
| 59 --indel-penalty=$computation.indel_penalty | |
| 60 #end if | |
| 61 #if $computation.indel_endlength.__str__ != '': | |
| 62 --indel-endlength=$computation.indel_endlength | |
| 63 #end if | |
| 64 #if $computation.max_middle_insertions.__str__ != '': | |
| 65 --max-middle-insertions=$computation.max_middle_insertions | |
| 66 #end if | |
| 67 #if $computation.max_middle_deletions.__str__ != '': | |
| 68 --max-middle-deletions=$computation.max_middle_deletions | |
| 69 #end if | |
| 70 #if $computation.max_end_insertions.__str__ != '': | |
| 71 --max-end-insertions=$computation.max_end_insertions | |
| 72 #end if | |
| 73 #if $computation.max_end_deletions.__str__ != '': | |
| 74 --max-end-deletions=$computation.max_end_deletions | |
| 75 #end if | |
| 76 #if $computation.suboptimal_levels.__str__ != '': | |
| 77 --suboptimal-levels=$computation.suboptimal_levels | |
| 78 #end if | |
| 79 #if $computation.adapter_strip.__str__ != '': | |
| 80 --adapter-strip=$computation.adapter_strip | |
| 81 #end if | |
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82 #if $computation.trim_mismatch_score.__str__ != '': |
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83 --trim-mismatch-score=$computation.trim_mismatch_score |
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84 #end if |
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85 ## TODO - do we need these options (Is it tally XOR runlength?): |
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86 ## --tallydir= --use-tally=tally |
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87 ## --runlengthdir --use-runlength=runlength |
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88 #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0: |
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89 ##--tallydir $os.path.dirname($computation.use_tally) --use-tally $os.path.basename($computation.use_tally) |
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90 --use-tally=$computation.use_tally |
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91 #end if |
| 0 | 92 ## gmap options |
| 93 #if $computation.gmap_mode.__str__ != '' and $computation.gmap_mode.__str__ != 'None': | |
| 94 --gmap-mode='$computation.gmap_mode' | |
| 95 #end if | |
| 96 #if $computation.trigger_score_for_gmap.__str__ != '': | |
| 97 --trigger-score-for-gmap=$computation.trigger_score_for_gmap | |
| 98 #end if | |
| 99 #if $computation.max_gmap_pairsearch.__str__ != '' and $re.search("pairsearch",$computation.gmap_mode): | |
| 100 --max-gmap-pairsearch=$computation.max_gmap_pairsearch | |
| 101 #end if | |
| 102 #if $computation.max_gmap_terminal.__str__ != '' and $re.search("terminal",$computation.gmap_mode): | |
| 103 --max-gmap-terminal=$computation.max_gmap_terminal | |
| 104 #end if | |
| 105 #if $computation.max_gmap_improvement.__str__ != '' and $re.search("improv",$computation.gmap_mode): | |
| 106 --max-gmap-improvement=$computation.max_gmap_improvement | |
| 107 #end if | |
| 108 #if $computation.microexon_spliceprob.__str__ != '': | |
| 109 --microexon-spliceprob=$computation.microexon_spliceprob | |
| 110 #end if | |
| 111 #end if | |
| 112 #if $splicing.options == "advanced": | |
| 113 $splicing.novelsplicing | |
| 114 #if $splicing.localsplicedist.__str__ != '': | |
| 115 --localsplicedist=$splicing.localsplicedist | |
| 116 #end if | |
| 117 #if $splicing.local_splice_penalty.__str__ != '': | |
| 118 --local-splice-penalty=$splicing.local_splice_penalty | |
| 119 #end if | |
| 120 #if $splicing.distant_splice_penalty.__str__ != '': | |
| 121 --distant-splice-penalty=$splicing.distant_splice_penalty | |
| 122 #end if | |
| 123 #if $splicing.local_splice_endlength.__str__ != '': | |
| 124 --local-splice-endlength=$splicing.local_splice_endlength | |
| 125 #end if | |
| 126 #if $splicing.distant_splice_endlength.__str__ != '': | |
| 127 --distant-splice-endlength=$splicing.distant_splice_endlength | |
| 128 #end if | |
| 129 #if $splicing.distant_splice_identity.__str__ != '': | |
| 130 --distant-splice-identity=$splicing.distant_splice_identity | |
| 131 #end if | |
| 132 #end if | |
| 133 #if $output.options == "advanced": | |
| 134 #if $output.npath.__str__ != '': | |
| 135 --npath=$output.npath | |
| 136 #end if | |
| 137 $output.quiet_if_excessive | |
| 138 $output.show_refdiff | |
| 139 $output.clip_overlap | |
| 140 #end if | |
| 141 #if $result.format == "sam": | |
| 142 --format=sam | |
| 143 $result.no_sam_headers | |
| 144 #if $result.read_group_id.__str__.strip != '': | |
| 145 --read-group-id='$result.read_group_id' | |
| 146 #end if | |
| 147 #if $result.read_group_name.__str__ != '': | |
| 148 --read-group-name='$result.read_group_name' | |
| 149 #end if | |
| 150 #if $result.read_group_library.__str__ != '': | |
| 151 --read-group-library='$result.read_group_library' | |
| 152 #end if | |
| 153 #if $result.read_group_platform.__str__ != '': | |
| 154 --read-group-platform='$result.read_group_platform' | |
| 155 #end if | |
| 156 #if $result.quality_shift.__str__ != '': | |
| 157 --quality-shift=$result.quality_shift | |
| 158 #end if | |
| 159 #elif $result.format == "goby": | |
| 160 #if $result.goby_output.__str__ != '': | |
| 161 --goby-output='$result.goby_output' | |
| 162 #end if | |
| 163 #if $result.creads_window_start.__str__ != '': | |
| 164 --creads-window-start=$result.creads_window_start | |
| 165 #end if | |
| 166 #if $result.creads_window_end.__str__ != '': | |
| 167 --creads-window-end=$result.creads_window_end | |
| 168 #end if | |
| 169 $result.creads_complement | |
| 170 #end if | |
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171 #if $results.split_output == 'yes': |
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172 --split-output=gsnap_out |
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173 #if $results.fails.choice == 'nofails': |
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174 --nofails |
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175 #elif $results.fails.choice == 'failsonly': |
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176 --failsonly |
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177 #end if |
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178 $results.fails_as_input |
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179 #else |
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180 #if $results.fails.choice == 'nofails': |
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181 --nofails |
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182 #elif $results.fails.choice == 'failsonly': |
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183 --failsonly |
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184 $results.fails.fails_as_input |
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185 #end if |
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186 #end if |
| 0 | 187 #if $seq.format == "gsnap_fasta": |
| 188 $seq.circularinput $seq.gsnap | |
| 189 #else if $seq.format == "fastq": | |
| 190 #if $seq.barcode_length.__str__ != '': | |
| 191 --barcode-length=$seq.barcode_length | |
| 192 #end if | |
| 193 #if $seq.fastq_id_start.__str__ != '': | |
| 194 --fastq-id-start=$seq.fastq_id_start | |
| 195 #end if | |
| 196 #if $seq.fastq_id_end.__str__ != '': | |
| 197 --fastq-id-end=$seq.fastq_id_end | |
| 198 #end if | |
| 199 #if $seq.filter_chastity.__str__ != 'off': | |
| 200 --filter-chastity=$seq.filter_chastity | |
| 201 #end if | |
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202 #if $seq.paired.ispaired.__str__ == 'yes': |
| 0 | 203 #if $seq.paired.pairmax_dna.__str__ != '': |
| 204 --pairmax-dna=$seq.paired.pairmax_dna | |
| 205 #end if | |
| 206 #if $seq.paired.pairmax_rna.__str__ != '': | |
| 207 --pairmax-rna=$seq.paired.pairmax_rna | |
| 208 #end if | |
| 209 $seq.fastq $seq.paired.fastq | |
| 210 #else | |
| 211 $seq.fastq | |
| 212 #end if | |
| 213 #end if | |
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214 #if $results.split_output == 'yes': |
| 0 | 215 2> $gsnap_stderr |
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216 #else: |
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217 #if $results.fails.choice.__str__ == 'failsonly' and $results.fails.fails_as_input.__str__ != '': |
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218 2> $gsnap_stderr > $gsnap_fq |
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219 #else |
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220 2> $gsnap_stderr > $gsnap_out |
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221 #end if |
| 0 | 222 #end if |
| 223 | |
| 224 </command> | |
| 225 <inputs> | |
| 226 <!-- Input data --> | |
| 227 <conditional name="seq"> | |
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228 <param name="format" type="select" label="<H2>Input Sequences</H2>Select the input format" help=""> |
| 0 | 229 <option value="fastq">Fastq</option> |
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230 <!-- |
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231 <option value="goby">Goby compact-reads</option> |
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232 --> |
| 0 | 233 <option value="gsnap_fasta">GNSAP fasta</option> |
| 234 </param> | |
| 235 <when value="fastq"> | |
| 236 <param name="fastq" type="data" format="fastq" label="Select a fastq dataset" /> | |
| 237 <conditional name="paired"> | |
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238 <param name="ispaired" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use Paired Reads?"/> |
| 0 | 239 <when value="no"/> |
| 240 <when value="yes"> | |
| 241 <param name="fastq" type="data" format="fastq" label="Select the paired reads reverse dataset" /> | |
| 242 <param name="orientation" type="select" label="Orientation of paired-end reads" help=""> | |
| 243 <option value="FR">fwd-rev, typical Illumina default</option> | |
| 244 <option value="RF">rev-fwd, for circularized inserts</option> | |
| 245 <option value="FF">fwd-fwd, same strand</option> | |
| 246 </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."/> | |
| 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."/> | |
| 249 </when> | |
| 250 </conditional> | |
| 251 <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" /> | |
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252 <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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253 <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, whitespace-delimited, starting from 1" |
| 0 | 254 help="Examples: |
| 255 <br>@HWUSI-EAS100R:6:73:941:1973#0/1 | |
| 256 <br> . start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0/1 | |
| 257 <br>@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 | |
| 258 <br> . start=1, end=1 => identifier is SRR001666.1 | |
| 259 <br> . start=2, end=2 => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345 | |
| 260 <br> . start=1, end=2 => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345" | |
| 261 /> | |
| 262 <param name="filter_chastity" type="select" label="Skip reads marked by the Illumina chastity program" | |
| 263 help="String after the accession having a 'Y' after the first colon, like this: | |
| 264 <br>@accession 1:Y:0:CTTGTA | |
| 265 <br>where the 'Y' signifies filtering by chastity. | |
| 266 <br> For 'either', a 'Y' on either end of a paired-end read will be filtered. | |
| 267 <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)" | |
| 268 > | |
| 269 <option value="off">off - no filtering</option> | |
| 270 <option value="either">either - a 'Y' on either end of a paired-end read</option> | |
| 271 <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> | |
| 272 </param> | |
| 273 </when> | |
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274 <!-- |
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275 <when value="goby"> |
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276 </when> |
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277 --> |
| 0 | 278 <when value="gsnap_fasta"> |
| 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"/> | |
| 280 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/> | |
| 281 </when> | |
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282 |
| 0 | 283 </conditional> |
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284 <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold" |
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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 |
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286 (if not selected, then reports all multiple results, up to npaths)" /> |
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287 |
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288 <!-- GMAPDB for alignment --> |
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289 <conditional name="refGenomeSource"> |
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290 <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"> |
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291 <option value="indexed">Use a built-in index</option> |
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292 <option value="gmapdb">Use a gmapdb from your history</option> |
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293 </param> |
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294 <when value="indexed"> |
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295 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> |
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296 <options from_file="gmap_indices.loc"> |
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297 <column name="uid" index="0" /> |
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298 <column name="dbkey" index="1" /> |
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299 <column name="name" index="2" /> |
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300 <column name="kmers" index="3" /> |
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301 <column name="maps" index="4" /> |
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302 <column name="snps" index="5" /> |
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303 <column name="value" index="6" /> |
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304 </options> |
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305 </param> |
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306 |
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307 <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> |
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308 <options from_file="gmap_indices.loc"> |
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309 <column name="name" index="3"/> |
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310 <column name="value" index="3"/> |
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311 <filter type="param_value" ref="gmapindex" column="6"/> |
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312 <filter type="multiple_splitter" column="3" separator=","/> |
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313 <filter type="add_value" name="" value=""/> |
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314 <filter type="sort_by" column="3"/> |
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315 </options> |
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316 </param> |
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317 |
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318 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase."> |
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319 <option value="">standard</option> |
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320 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> |
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321 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> |
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322 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option> |
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323 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option> |
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324 </param> |
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325 |
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326 <conditional name="use_splicing"> |
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327 <param name="src" type="select" label="<HR>Known Splicesite and Introns" |
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328 help="Look for splicing involving known sites or known introns at short or long distances |
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329 See README instructions for the distinction between known sites and known introns"> |
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330 <option value="none" selected="true">None</option> |
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331 <option value="gmapdb">From the GMAP Database</option> |
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332 <option value="history">A Map in your history</option> |
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333 </param> |
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334 <when value="none"/> |
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335 <when value="history"> |
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336 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" |
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337 help="built with GMAP IIT"/> |
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338 </when> |
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339 <when value="gmapdb"> |
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340 <param name="splicemap" type="select" data_ref="gmapindex" label="Use map for splicing involving known sites or known introns" help=""> |
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341 <options from_file="gmap_indices.loc"> |
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342 <column name="name" index="4"/> |
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343 <column name="value" index="4"/> |
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344 <filter type="param_value" ref="gmapindex" column="6"/> |
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345 <filter type="multiple_splitter" column="4" separator=","/> |
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346 <filter type="add_value" name="" value=""/> |
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347 <filter type="sort_by" column="4"/> |
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348 </options> |
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349 </param> |
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350 </when> |
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351 </conditional> |
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352 |
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353 <conditional name="use_snps"> |
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354 <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments"> |
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355 <option value="none" selected="true">None</option> |
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356 <option value="gmapdb">From the GMAP Database</option> |
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357 <option value="history">A SNP Index in your history</option> |
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358 </param> |
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359 <when value="none"/> |
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360 <when value="history"> |
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361 <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex" |
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362 help="built with GMAP SNP Index"/> |
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363 </when> |
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364 <when value="gmapdb"> |
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365 <param name="snpindex" type="select" data_ref="gmapindex" label="Use database containing known SNPs" help=""> |
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366 <options from_file="gmap_indices.loc"> |
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367 <column name="name" index="5"/> |
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368 <column name="value" index="5"/> |
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369 <filter type="param_value" ref="gmapindex" column="6"/> |
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370 <filter type="multiple_splitter" column="5" separator=","/> |
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371 <filter type="add_value" name="" value=""/> |
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372 <filter type="sort_by" column="5"/> |
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373 </options> |
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374 </param> |
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375 </when> |
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376 </conditional> |
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377 |
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378 </when> |
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379 <when value="gmapdb"> |
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380 <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" |
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381 help="A GMAP database built with GMAP Build"/> |
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382 <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> |
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383 <options> |
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384 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> |
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385 </options> |
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386 </param> |
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387 |
|
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388 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase."> |
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389 <option value="">standard</option> |
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390 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> |
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391 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> |
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392 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option> |
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393 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option> |
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394 </param> |
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395 |
|
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396 <conditional name="use_splicing"> |
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397 <param name="src" type="select" label="<HR>Known Splicesite and Introns" |
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398 help="Look for splicing involving known sites or known introns at short or long distances |
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399 See README instructions for the distinction between known sites and known introns"> |
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400 <option value="none" selected="true">None</option> |
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401 <option value="gmapdb">From the GMAP Database</option> |
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402 <option value="history">A Map in your history</option> |
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403 </param> |
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404 <when value="none"/> |
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405 <when value="history"> |
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406 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" |
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407 help="built with GMAP IIT"/> |
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408 </when> |
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409 <when value="gmapdb"> |
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410 <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> |
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411 <options> |
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412 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> |
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413 </options> |
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414 </param> |
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415 </when> |
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416 </conditional> |
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417 |
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418 <conditional name="use_snps"> |
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419 <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments"> |
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420 <option value="none" selected="true">None</option> |
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421 <option value="gmapdb">From the GMAP Database</option> |
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422 <option value="history">A SNP Index in your history</option> |
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423 </param> |
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424 <when value="none"/> |
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425 <when value="history"> |
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426 <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex" |
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427 help="built with GMAP SNP Index"/> |
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428 </when> |
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429 <when value="gmapdb"> |
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430 <param name="snpindex" type="select" data_ref="gmapdb" label="Use database containing known SNPs" help=""> |
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431 <options> |
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432 <filter type="data_meta" ref="gmapdb" key="snps" multiple="True" separator=","/> |
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433 </options> |
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434 </param> |
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435 </when> |
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436 </conditional> |
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437 |
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438 </when> |
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439 </conditional> |
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440 |
| 0 | 441 <!-- Computation options --> |
| 442 <conditional name="computation"> | |
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443 <param name="options" type="select" label="<HR>Computational Settings" help=""> |
| 0 | 444 <option value="default">Use default settings</option> |
| 445 <option value="advanced">Set Computation Options</option> | |
| 446 </param> | |
| 447 <when value="default"/> | |
| 448 <when value="advanced"> | |
| 449 <param name="max_mismatches" type="float" value="" optional="true" label="Maximum number of mismatches allowed (uses default when negative)" | |
| 450 help="Defaults to the ultrafast level of ((readlength+2)/12 - 2)). | |
| 451 If specified between 0.0 and 1.0, then treated as a fraction | |
| 452 of each read length. Otherwise, treated as an integral number | |
| 453 of mismatches (including indel and splicing penalties) | |
| 454 For RNA-Seq, you may need to increase this value slightly | |
| 455 to align reads extending past the ends of an exon."> | |
| 456 <validator type="in_range" message="The mismatches must >= 0." min="0."/> | |
| 457 </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"/> | |
| 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"/> | |
| 460 <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 3)" | |
| 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." /> | |
| 462 <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 < 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)" /> | |
| 465 <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)" /> | |
| 467 <param name="max_end_insertions" type="integer" value="" optional="true" label="Maximum number of end insertions allowed (default 3)" /> | |
| 468 <param name="max_end_deletions" type="integer" value="" optional="true" label="Maximum number of end deletions allowed (default 6)" /> | |
| 469 <param name="suboptimal_levels" type="integer" value="" optional="true" label="Report suboptimal hits beyond best hit (default 0)" | |
| 470 help="All hits with best score plus suboptimal-levels are reported" /> | |
| 471 <param name="adapter_strip" type="select" label="Method for removing adapters from reads" | |
| 472 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> | |
| 474 <option value="off">off</option> | |
| 475 </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)" | |
| 477 help="to turn off trimming, specify 0"/> | |
|
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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" |
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479 help="generated by gsnap_tally and iit_store"/> |
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480 |
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481 <!-- |
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482 tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is |
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483 location of genome index files specified using -D and -d). Note: can |
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484 just give full path name to use-tally instead. |
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485 use-tally=STRING Use this tally IIT file to resolve concordant multiple results |
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486 runlengthdir=STRING Directory for runlength IIT file to resolve concordant multiple results (default is |
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487 location of genome index files specified using -D and -d). Note: can |
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488 just give full path name to use-runlength instead. |
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489 use-runlength=STRING Use this runlength IIT file to resolve concordant multiple results |
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490 --> |
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491 |
| 0 | 492 <!-- Options for GMAP alignment within GSNAP --> |
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493 <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" |
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494 help="Default: pairsearch,terminal,improve"> |
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495 <option value="pairsearch" selected="true">pairsearch</option> |
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496 <option value="terminal" selected="true">terminal</option> |
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497 <option value="improve" selected="true">improve</option> |
| 0 | 498 </param> |
| 499 <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)" | |
| 500 help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" /> | |
| 501 <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)" | |
| 502 help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." /> | |
| 503 <param name="max_gmap_terminal" type="integer" value="" optional="true" label="GMAP terminal threshold (default 3)" | |
| 504 help="Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 3)." /> | |
| 505 <param name="max_gmap_improvement" type="integer" value="" optional="true" label="GMAP improvement threshold (default 3)" | |
| 506 help="Perform GMAP improvement on nearby genomic regions up to this many candidate ends (default 3)." /> | |
| 507 <param name="microexon_spliceprob" type="float" value="" optional="true" label="GMAP microexons threshold (default .90)" | |
| 508 help="Allow microexons only if one of the splice site probabilities is greater than this value." > | |
| 509 <validator type="in_range" message="The microexons probability must be between 0. and 1." min="0." max="1."/> | |
| 510 </param> | |
| 511 </when> | |
| 512 </conditional> | |
| 513 | |
| 514 <conditional name="splicing"> | |
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515 <param name="options" type="select" label="<HR>Splicing options for RNA-Seq" help=""> |
| 0 | 516 <option value="default">Use default settings</option> |
| 517 <option value="advanced">Set Splicing Options</option> | |
| 518 </param> | |
| 519 <when value="default"/> | |
| 520 <when value="advanced"> | |
| 521 <!-- Splicing options for RNA-Seq --> | |
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522 <!-- use-splicing This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splicing --> |
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523 <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) --> |
| 0 | 524 <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/> |
| 525 <param name="localsplicedist" type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/> | |
| 526 <param name="local_splice_penalty" type="integer" value="" optional="true" label="Penalty for a local splice (default 0). Counts against mismatches allowed"/> | |
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527 <param name="distant_splice_penalty" type="integer" value="" optional="true" label="Penalty for a distant splice (default 3). Counts against mismatches allowed" |
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528 help="A distant splice is one where the intron length exceeds the value of localsplicedist or is an |
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529 inversion, scramble, or translocation between two different chromosomes. Counts against mismatches allowed"/> |
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530 <param name="distant_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments" |
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531 help="(default 16, min is the kmer length)"/> |
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532 <param name="shortend_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for short-end spliced alignments" |
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533 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"/> |
| 0 | 534 <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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535 <param name="antistranded_penalty" type="integer" value="" optional="true" label="Penalty for antistranded splicing when using stranded RNA-Seq protocols" |
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536 help="A positive value, such as 1, expects antisense on the first read and sense on the second read. |
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537 Default is 0, which treats sense and antisense equally well"/> |
| 0 | 538 </when> |
| 539 </conditional> | |
| 540 | |
| 541 <!-- Output data --> | |
| 542 <conditional name="output"> | |
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543 <param name="options" type="select" label="<HR><H2>Output</H2>Output options for RNA-Seq" help=""> |
| 0 | 544 <option value="default">Use default settings</option> |
| 545 <option value="advanced">Set Output Options</option> | |
| 546 </param> | |
| 547 <when value="default"/> | |
| 548 <when value="advanced"> | |
| 549 <param name="npath" type="integer" value="" optional="true" label="Maximum number of paths to print (default 100)"/> | |
| 550 <param name="quiet_if_excessive" type="boolean" checked="false" truevalue="--quiet-if-excessive" falsevalue="" label="Quiet if Excessive" | |
| 551 help="If more than maximum number of paths are found, then nothing is printed."/> | |
| 552 <param name="show_refdiff" type="boolean" checked="false" truevalue="--show-refdiff" falsevalue="" label="Show SNP-tolerant alignment" | |
| 553 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)"/> | |
| 554 <param name="clip_overlap" type="boolean" checked="false" truevalue="--clip-overlap" falsevalue="" label="Clip Overlap" | |
| 555 help="For paired-end reads whose alignments overlap, clip the overlapping region."/> | |
| 556 </when> | |
| 557 </conditional> | |
| 558 <conditional name="result"> | |
| 559 <param name="format" type="select" label="Select the output format" help=""> | |
| 560 <option value="sam">SAM</option> | |
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561 <!-- goby should only be an option if the input is in goby format |
| 0 | 562 <option value="goby">Goby</option> |
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563 --> |
| 0 | 564 <option value="gsnap">GSNAP default output</option> |
| 565 </param> | |
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566 <when value="gsnap"> |
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567 </when> |
| 0 | 568 <when value="sam"> |
| 569 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> | |
| 570 <param name="read_group_id" type="text" value="" optional="true" label="Value to put into read-group id (RG-ID) field"/> | |
| 571 <param name="read_group_name" type="text" value="" optional="true" label="Value to put into read-group name (RG-SM) field"/> | |
| 572 <param name="read_group_library" type="text" value="" optional="true" label="Value to put into read-group library (RG-LB) field"/> | |
| 573 <param name="read_group_platform" type="text" value="" optional="true" label="Value to put into read-group library platform (RG-PL) field"/> | |
| 574 <param name="quality_shift" type="integer" value="" optional="true" label="Shift FASTQ quality scores by this amount in SAM output (default -31)"/> | |
| 575 </when> | |
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576 <!-- |
| 0 | 577 <when value="goby"> |
| 578 <param name="goby_output" type="text" value="" label="Basename for Goby output files"/> | |
| 579 <param name="creads_window_start" type="integer" value="" optional="true" label="Compact reads window start (default: 0=start of file)"/> | |
| 580 <param name="creads_window_end" type="integer" value="" optional="true" label="Compact reads window end (default: 0=end of file)"/> | |
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581 <param name="creads_complement" type="boolean" truevalue="-\-creads-complement" falsevalue="" checked="false" label="Complement read sequences (without reversing)"/> |
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582 </when> |
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583 --> |
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584 </conditional> |
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585 <!-- TODO combine fails and split_output --> |
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586 |
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587 <conditional name="results"> |
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588 <param name="split_output" type="select" label="<HR>Split outputs" |
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589 help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results"> |
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590 <option value="no">no</option> |
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591 <option value="yes">yes</option> |
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592 </param> |
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593 <when value="no"> |
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594 <conditional name="fails"> |
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595 <param name="choice" type="select" label="How to deal with fails" help=""> |
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596 <option value="default">default - include them in results</option> |
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597 <option value="nofails">nofails - exclude fails from results</option> |
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598 <option value="failsonly">failsonly - only output failing results</option> |
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599 </param> |
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600 <when value="default"/> |
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601 <when value="nofails"/> |
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602 <when value="failsonly"> |
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603 <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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604 help=""/> |
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605 </when> |
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606 </conditional> |
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607 </when> |
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608 <when value="yes"> |
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609 <conditional name="fails"> |
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610 <param name="choice" type="select" label="How to deal with fails" help=""> |
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611 <option value="default">default - include them in results</option> |
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612 <option value="nofails">nofails - exclude fails from results</option> |
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613 <option value="failsonly">failsonly - only output failing results</option> |
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614 </param> |
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615 <when value="default"/> |
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616 <when value="nofails"/> |
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617 <when value="failsonly"/> |
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618 </conditional> |
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619 <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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620 help=""/> |
| 0 | 621 </when> |
| 622 </conditional> | |
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623 |
| 0 | 624 </inputs> |
| 625 <outputs> | |
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626 <data format="txt" name="gsnap_stderr" label="${tool.name} on ${on_string}: gsnap.log"/> |
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627 |
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628 <data format="txt" name="gsnap_out" label="${tool.name} on ${on_string} ${result.format}" > |
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629 <filter>(results['split_output'] == 'no' and (results['fails']['choice'] != 'failsonly' or results['fails']['fails_as_input'] == False))</filter> |
| 0 | 630 <change_format> |
| 631 <when input="result['format']" value="sam" format="sam"/> | |
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632 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 633 </change_format> |
| 634 </data> | |
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635 |
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636 <data format="fastq" name="gsnap_fq" label="${tool.name} on ${on_string} fails.fq" > |
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637 <filter>(results['split_output'] == 'no' and results['fails']['choice'] == 'failsonly' and results['fails']['fails_as_input'] == True)</filter> |
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638 </data> |
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639 |
| 0 | 640 <!-- nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, concordant_mult --> |
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641 |
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642 <data format="txt" name="unpaired_mult" label="${tool.name} on ${on_string} unpaired_mult.${result.format}" from_work_dir="gsnap_out.unpaired_mult"> |
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643 <filter>(results['split_output'] == 'yes')</filter> |
| 0 | 644 <change_format> |
| 645 <when input="result['format']" value="sam" format="sam"/> | |
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646 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 647 </change_format> |
| 648 </data> | |
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649 <data format="txt" name="unpaired_uniq" label="${tool.name} on ${on_string} unpaired_uniq.${result.format}" from_work_dir="gsnap_out.unpaired_uniq"> |
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650 <filter>(results['split_output'] == 'yes')</filter> |
| 0 | 651 <change_format> |
| 652 <when input="result['format']" value="sam" format="sam"/> | |
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653 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 654 </change_format> |
| 655 </data> | |
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656 <data format="txt" name="unpaired_transloc" label="${tool.name} on ${on_string} unpaired_transloc.${result.format}" from_work_dir="gsnap_out.unpaired_transloc"> |
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657 <filter>(results['split_output'] == 'yes')</filter> |
| 0 | 658 <change_format> |
| 659 <when input="result['format']" value="sam" format="sam"/> | |
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660 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 661 </change_format> |
| 662 </data> | |
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663 <data format="txt" name="halfmapping_mult" label="${tool.name} on ${on_string} halfmapping_mult.${result.format}" from_work_dir="gsnap_out.halfmapping_mult"> |
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664 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
| 0 | 665 <change_format> |
| 666 <when input="result['format']" value="sam" format="sam"/> | |
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667 <when input="result['format']" value="gsnap" format="gsnap"/> |
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668 </change_format> |
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669 </data> |
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670 <data format="txt" name="halfmapping_uniq" label="${tool.name} on ${on_string} halfmapping_uniq.${result.format}" from_work_dir="gsnap_out.halfmapping_uniq"> |
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671 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
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672 <change_format> |
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673 <when input="result['format']" value="sam" format="sam"/> |
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674 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 675 </change_format> |
| 676 </data> | |
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677 <data format="txt" name="halfmapping_transloc" label="${tool.name} on ${on_string} halfmapping_transloc.${result.format}" from_work_dir="gsnap_out.halfmapping_transloc"> |
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678 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
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679 <change_format> |
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680 <when input="result['format']" value="sam" format="sam"/> |
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681 <when input="result['format']" value="gsnap" format="gsnap"/> |
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682 </change_format> |
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683 </data> |
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684 <data format="txt" name="paired_mult" label="${tool.name} on ${on_string} paired_mult.${result.format}" from_work_dir="gsnap_out.paired_mult"> |
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685 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
| 0 | 686 <change_format> |
| 687 <when input="result['format']" value="sam" format="sam"/> | |
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688 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 689 </change_format> |
| 690 </data> | |
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691 <data format="txt" name="paired_uniq" label="${tool.name} on ${on_string} paired_uniq.${result.format}" from_work_dir="gsnap_out.paired_uniq"> |
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692 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
| 0 | 693 <change_format> |
| 694 <when input="result['format']" value="sam" format="sam"/> | |
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695 <when input="result['format']" value="gsnap" format="gsnap"/> |
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696 </change_format> |
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697 </data> |
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698 <data format="txt" name="paired_transloc" label="${tool.name} on ${on_string} paired_transloc.${result.format}" from_work_dir="gsnap_out.paired_transloc"> |
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699 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
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700 <change_format> |
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701 <when input="result['format']" value="sam" format="sam"/> |
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702 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 703 </change_format> |
| 704 </data> | |
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705 |
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706 <data format="txt" name="concordant_mult" label="${tool.name} on ${on_string} concordant_mult.${result.format}" from_work_dir="gsnap_out.concordant_mult"> |
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707 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
| 0 | 708 <change_format> |
| 709 <when input="result['format']" value="sam" format="sam"/> | |
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710 <when input="result['format']" value="gsnap" format="gsnap"/> |
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711 </change_format> |
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712 </data> |
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713 <data format="txt" name="concordant_uniq" label="${tool.name} on ${on_string} concordant_uniq.${result.format}" from_work_dir="gsnap_out.concordant_uniq"> |
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714 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
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715 <change_format> |
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716 <when input="result['format']" value="sam" format="sam"/> |
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717 <when input="result['format']" value="gsnap" format="gsnap"/> |
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718 </change_format> |
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719 </data> |
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720 <data format="txt" name="concordant_transloc" label="${tool.name} on ${on_string} concordant_transloc.${result.format}" from_work_dir="gsnap_out.concordant_transloc"> |
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721 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
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722 <change_format> |
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723 <when input="result['format']" value="sam" format="sam"/> |
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724 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 725 </change_format> |
| 726 </data> | |
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727 |
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728 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gsnap_out.nomapping"> |
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729 <filter>(results['split_output'] == 'yes' and results['fails_as_input'] == False)</filter> |
| 0 | 730 <change_format> |
| 731 <when input="result['format']" value="sam" format="sam"/> | |
|
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732 <when input="result['format']" value="gsnap" format="gsnap"/> |
| 0 | 733 </change_format> |
| 734 </data> | |
|
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735 |
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736 <data format="fastq" name="nomapping_fq" label="${tool.name} on ${on_string} nomapping.fq" from_work_dir="gsnap_out.nomapping.fq"> |
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737 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == False)</filter> |
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738 </data> |
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739 |
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740 <data format="fastq" name="nomapping_1_fq" label="${tool.name} on ${on_string} nomapping.1.fq" from_work_dir="gsnap_out.nomapping.1.fq"> |
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741 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
| 0 | 742 </data> |
| 743 | |
|
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744 <data format="fastq" name="nomapping_2_fq" label="${tool.name} on ${on_string} nomapping.2.fq" from_work_dir="gsnap_out.nomapping.2.fq"> |
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745 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> |
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746 </data> |
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747 |
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748 <!-- Will problay need wrapper code to generate composite datatype for goby alignment |
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749 <data format="gobyalignment" name="goby_alignment" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.nomapping"> |
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750 <filter>result['format'] == 'goby'</filter> |
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751 </data> |
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752 --> |
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753 |
| 0 | 754 </outputs> |
| 755 <tests> | |
| 756 </tests> | |
| 757 | |
| 758 <help> | |
| 759 | |
| 760 **What it does** | |
| 761 | |
| 762 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. | |
| 763 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. | |
| 764 | |
| 765 .. _GSNAP: http://research-pub.gene.com/gmap/ | |
| 766 .. _Publication: http://bioinformatics.oupjournals.org/cgi/content/full/26/7/873 | |
| 767 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed | |
| 768 | |
| 769 ------ | |
| 770 | |
| 771 **Know what you are doing** | |
| 772 | |
| 773 .. class:: warningmark | |
| 774 | |
| 775 You will want to read the README_ | |
| 776 | |
| 777 .. _README: http://research-pub.gene.com/gmap/src/README | |
| 778 | |
| 779 ------ | |
| 780 | |
| 781 **Input formats** | |
| 782 | |
| 783 Input to GSNAP should be either in FASTQ or FASTA format. | |
| 784 | |
| 785 The FASTQ input may include quality scores, which will then be included in SAM | |
| 786 output, if that output format is selected. | |
| 787 | |
| 788 For FASTA format, you should include one line per read (or end of a | |
| 789 paired-end read). The same FASTA file can have a mixture of | |
| 790 single-end and paired-end reads of varying lengths, if desired. | |
| 791 | |
| 792 Single-end reads: | |
| 793 | |
| 794 Each FASTA entry should contain one short read per line, like this | |
| 795 | |
| 796 >Header information | |
| 797 AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA | |
| 798 | |
| 799 Each short read can have a different length. However, the entire read | |
| 800 needs to be on a single line, and may not wrap around multiple lines. | |
| 801 If it extends to a second line, GSNAP will think that the read is | |
| 802 paired-end. | |
| 803 | |
| 804 | |
| 805 Paired-end reads: | |
| 806 | |
| 807 Each FASTA entry should contain two short reads, one per line, like | |
| 808 this | |
| 809 | |
| 810 >Header information | |
| 811 AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA | |
| 812 GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG | |
| 813 | |
| 814 By default, the program assumes that the second end is in the reverse | |
| 815 complement direction compared with the first end. If they are in the | |
| 816 same direction, you may need to use the --circular-input (or -c) flag. | |
| 817 | |
| 818 ( The Galaxy tool: "FASTA Width formatter" can be used to reformat fasta files to have single line sequences. ) | |
| 819 | |
| 820 ------ | |
| 821 | |
| 822 **Output formats in GSNAP** | |
| 823 | |
| 824 SAM output format | |
| 825 | |
| 826 Default GSNAP format | |
| 827 See the README_ | |
| 828 | |
| 829 | |
| 830 | |
| 831 | |
| 832 </help> | |
| 833 </tool> | |
| 834 |