Mercurial > repos > jjohnson > gmap
annotate gmap.xml @ 5:14561eb803a5 draft
Uploaded v3.0.1b (still working on this prior to main Tool Shed release)
| author | peterjc |
|---|---|
| date | Fri, 21 Oct 2016 10:55:40 -0400 |
| parents | 488e9d642566 |
| children |
| rev | line source |
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1 <tool id="gmap" name="GMAP" version="3.0.1"> |
| 0 | 2 <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</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>gmap --version</version_command> |
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7 <command detect_errors="exit_code"><![CDATA[ |
| 0 | 8 #import os,os.path |
| 9 gmap | |
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10 --nthreads=\${GALAXY_SLOTS:-4} --ordered |
| 0 | 11 #if $refGenomeSource.genomeSource == "history": |
| 12 --gseg=$refGenomeSource.ownFile | |
| 13 #elif $refGenomeSource.genomeSource == "gmapdb": | |
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14 --dir='$refGenomeSource.gmapdb.extra_files_path' --db='$refGenomeSource.gmapdb.metadata.db_name' |
| 0 | 15 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: |
| 16 --kmer=$refGenomeSource.kmer | |
| 17 #end if | |
| 18 #else: | |
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19 --dir='$os.path.dirname($refGenomeSource.gmapindex.value)' --db='$os.path.basename($refGenomeSource.gmapindex.value)' |
| 0 | 20 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: |
| 21 --kmer=$refGenomeSource.kmer | |
| 22 #end if | |
| 23 #end if | |
| 24 #if $result.format == "summary": | |
| 25 --summary | |
| 26 #elif $result.format == "align": | |
| 27 --align | |
| 28 #elif $result.format == "continuous": | |
| 29 --continuous | |
| 30 #elif $result.format == "continuous-by-exon": | |
| 31 --continuous-by-exon | |
| 32 #elif $result.format == "compress": | |
| 33 --compress | |
| 34 #elif $result.format == "exons_dna": | |
| 35 --exons=cdna | |
| 36 #elif $result.format == "exons_gen": | |
| 37 --exons=genomic | |
| 38 #elif $result.format == "protein_dna": | |
| 39 --protein_dna | |
| 40 #elif $result.format == "protein_gen": | |
| 41 --protein_gen | |
| 42 #elif $result.format == "sam": | |
| 43 --format=$result.sam_paired_read | |
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44 $result.no_sam_headers |
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45 $result.sam_use_0M |
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46 $result.force_xs_dir |
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47 $result.md_lowercase_snp |
| 0 | 48 #if len($result.read_group_id.__str__) > 0 |
| 49 --read-group-id=$result.read_group_id | |
| 50 #end if | |
| 51 #if len($result.read_group_name.__str__) > 0 | |
| 52 --read-group-name=$result.read_group_name | |
| 53 #end if | |
| 54 #if len($result.read_group_library.__str__) > 0 | |
| 55 --read-group-library=$result.read_group_library | |
| 56 #end if | |
| 57 #if len($result.read_group_platform.__str__) > 0 | |
| 58 --read-group-platform=$result.read_group_platform | |
| 59 #end if | |
| 60 #elif $result.format != "gmap": | |
| 61 --format=$result.format | |
| 62 #end if | |
| 63 #if $computation.options == "advanced": | |
| 64 $computation.nosplicing | |
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65 $computation.find_shifted_canonical |
| 0 | 66 $computation.cross_species |
| 67 #if len($computation.min_intronlength.__str__) > 0 | |
| 68 --min-intronlength=$computation.min_intronlength | |
| 69 #end if | |
| 70 #if len($computation.intronlength.__str__) > 0 | |
| 71 --intronlength=$computation.intronlength | |
| 72 #end if | |
| 73 #if len($computation.localsplicedist.__str__) > 0 | |
| 74 --localsplicedist=$computation.localsplicedist | |
| 75 #end if | |
| 76 #if len($computation.totallength.__str__) > 0 | |
| 77 --totallength=$computation.totallength | |
| 78 #end if | |
| 79 #if len($computation.trimendexons.__str__) > 0 | |
| 80 --trimendexons=$computation.trimendexons | |
| 81 #end if | |
| 82 --direction=$computation.direction | |
| 83 --canonical-mode=$computation.canonical | |
| 84 --prunelevel=$computation.prunelevel | |
| 85 --allow-close-indels=$computation.allow_close_indels | |
| 86 #if len($computation.microexon_spliceprob.__str__) >= 0: | |
| 87 --microexon-spliceprob=$computation.microexon_spliceprob | |
| 88 #end if | |
| 89 #if len($computation.chimera_margin.__str__) >= 0: | |
| 90 --chimera-margin=$computation.chimera_margin | |
| 91 #end if | |
| 92 #end if | |
| 93 #if $advanced.options == "used": | |
| 94 #if len($advanced.npaths.__str__) > 0: | |
| 95 --npaths=$advanced.npaths | |
| 96 #end if | |
| 97 #if len($advanced.suboptimal_score.__str__) > 0: | |
| 98 --suboptimal-score=$advanced.suboptimal_score | |
| 99 #end if | |
| 100 #if len($advanced.chimera_overlap.__str__) > 0: | |
| 101 --chimera_overlap=$advanced.chimera_overlap | |
| 102 #end if | |
| 103 $advanced.protein | |
| 104 $advanced.tolerant | |
| 105 $advanced.nolengths | |
| 106 $advanced.invertmode | |
| 107 #if len($advanced.introngap.__str__) > 0: | |
| 108 --introngap=$advanced.introngap | |
| 109 #end if | |
| 110 #if len($advanced.wraplength.__str__) > 0: | |
| 111 --wraplength=$advanced.wraplength | |
| 112 #end if | |
| 113 #end if | |
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114 $split_output |
| 0 | 115 #if len($quality_protocol.__str__) > 0: |
| 116 --quality-protocol=$quality_protocol | |
| 117 #end if | |
| 118 $input | |
| 119 #for $i in $inputs: | |
| 120 ${i.added_input} | |
| 121 #end for | |
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122 #if $split_output |
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123 2> $gmap_stderr |
| 0 | 124 #else |
| 125 2> $gmap_stderr > $output | |
| 126 #end if | |
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127 ]]></command> |
| 0 | 128 <inputs> |
| 129 <!-- Input data --> | |
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130 <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="Input Sequences" help="Select an mRNA or EST dataset to map" /> |
| 0 | 131 <repeat name="inputs" title="addtional mRNA or EST dataset to map"> |
| 132 <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/> | |
| 133 </repeat> | |
| 134 <param name="quality_protocol" type="select" label="Protocol for input quality scores"> | |
| 135 <option value="">No quality scores</option> | |
| 136 <option value="sanger">Sanger quality scores</option> | |
| 137 <option value="illumina">Illumina quality scores</option> | |
| 138 </param> | |
| 139 | |
| 140 <!-- GMAPDB for mapping --> | |
| 141 <conditional name="refGenomeSource"> | |
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142 <param name="genomeSource" type="select" label="Map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
| 0 | 143 <option value="indexed">Use a built-in index</option> |
| 144 <option value="gmapdb">Use gmapdb from the history</option> | |
| 145 <option value="history">Use a fasta reference sequence from the history</option> | |
| 146 </param> | |
| 147 <when value="indexed"> | |
| 148 <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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149 <options from_data_table="gmap_indices"> |
| 0 | 150 <column name="uid" index="0" /> |
| 151 <column name="dbkey" index="1" /> | |
| 152 <column name="name" index="2" /> | |
| 153 <column name="kmers" index="3" /> | |
| 154 <column name="maps" index="4" /> | |
| 155 <column name="snps" index="5" /> | |
| 156 <column name="value" index="6" /> | |
| 157 </options> | |
| 158 </param> | |
| 159 <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> | |
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160 <options from_data_table="gmap_indices"> |
| 0 | 161 <column name="name" index="3"/> |
| 162 <column name="value" index="3"/> | |
| 163 <filter type="param_value" ref="gmapindex" column="6"/> | |
| 164 <filter type="multiple_splitter" column="3" separator=","/> | |
| 165 <filter type="add_value" name="" value=""/> | |
| 166 <filter type="sort_by" column="3"/> | |
| 167 </options> | |
| 168 </param> | |
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169 <!-- |
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170 basesize=INT Base size to use in genome database. If not specified, the program |
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171 will find the highest available base size in the genome database |
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172 within selected k-mer size |
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173 sampling=INT Sampling to use in genome database. If not specified, the program |
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174 will find the smallest available sampling value in the genome database |
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175 within selected basesize and k-mer size |
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176 |
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177 --> |
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178 <!-- Not currently used in the command tag, |
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179 <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" > |
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180 <options from_data_table="gmap_indices"> |
| 0 | 181 <column name="name" index="4"/> |
| 182 <column name="value" index="4"/> | |
| 183 <filter type="param_value" ref="gmapindex" column="6"/> | |
| 184 <filter type="multiple_splitter" column="4" separator=","/> | |
| 185 <filter type="add_value" name="" value=""/> | |
| 186 <filter type="sort_by" column="4"/> | |
| 187 </options> | |
| 188 </param> | |
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189 --> |
| 0 | 190 </when> |
| 191 <when value="gmapdb"> | |
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192 <param name="gmapdb" type="data" format="gmapdb" label="Select a gmapdb" |
| 0 | 193 help="A GMAP database built with GMAP Build"/> |
| 194 <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> | |
| 195 <options> | |
| 196 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> | |
| 197 </options> | |
| 198 </param> | |
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199 <!-- Not currently used in the command tag, |
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200 <param name="map" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" > |
| 0 | 201 <options> |
| 202 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> | |
| 203 </options> | |
| 204 </param> | |
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205 --> |
| 0 | 206 </when> |
| 207 <when value="history"> | |
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208 <param name="ownFile" type="data" format="fasta" label="Select the reference genome" |
| 0 | 209 help="Fasta containing genomic DNA sequence"/> |
| 210 </when> | |
| 211 </conditional> | |
| 212 | |
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213 |
| 0 | 214 <!-- Computation options --> |
| 215 <conditional name="computation"> | |
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216 <param name="options" type="select" label="Computational Settings" > |
| 0 | 217 <option value="default">Use default settings</option> |
| 218 <option value="advanced">Set Computation Options</option> | |
| 219 </param> | |
| 220 <when value="default"/> | |
| 221 <when value="advanced"> | |
| 222 <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/> | |
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223 <param name="min_intronlength" type="integer" value="" optional="true" label="Min length for one internal intron (default 9)." help="Below this size, a genomic gap will be considered a deletion rather than an intron." > |
| 0 | 224 <validator type="in_range" message="min_intronlength must be positive" min="0" /> |
| 225 </param> | |
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226 <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" > |
| 0 | 227 <validator type="in_range" message="intronlength must be positive" min="0" /> |
| 228 </param> | |
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229 <param name="localsplicedist" type="integer" value="" optional="true" label="Max length for known splice sites at ends of sequence (default 200000)" > |
| 0 | 230 <validator type="in_range" message="localsplicedist must be positive" min="0" /> |
| 231 </param> | |
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232 <param name="totallength" type="integer" value="" optional="true" label="Max total intron length (default 2400000)" > |
| 0 | 233 <validator type="in_range" message="totallength must be positive" min="0" /> |
| 234 </param> | |
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235 <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera" |
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236 help=" default is 40, To turn off, set to 0" > |
| 0 | 237 <validator type="in_range" message="chimera_margin must be positive" min="0" /> |
| 238 </param> | |
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239 <param name="direction" type="select" label="cDNA direction"> |
| 0 | 240 <option value="auto">auto</option> |
| 241 <option value="sense_force">sense_force</option> | |
| 242 <option value="antisense_force">antisense_force</option> | |
| 243 <option value="sense_filter">sense_filter</option> | |
| 244 <option value="antisense_filter">antisense_filter</option> | |
| 245 </param> | |
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246 <param name="trimendexons" type="integer" value="" optional="true" label="Trim end exons with fewer than given number of matches (in nt, default 12)" > |
| 0 | 247 <validator type="in_range" message="trimendexons must be positive" min="1" /> |
| 248 </param> | |
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249 <param name="find_shifted_canonical" type="boolean" truevalue="--find-shifted-canonical-species" falsevalue="" checked="false" label="find-shifted-canonical Use a more sensitive search for canonical splicing" /> |
| 0 | 250 <param name="cross_species" type="boolean" truevalue="--cross-species" falsevalue="" checked="false" label="Cross-species alignment" help="For cross-species alignments, use a more sensitive search for canonical splicing"/> |
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251 |
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252 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns"> |
| 0 | 253 <option value="1">high reward (default)</option> |
| 254 <option value="0">low reward</option> | |
| 255 <option value="2">low reward for high-identity sequences</option> | |
| 256 </param> | |
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257 <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other"> |
| 0 | 258 <option value="1" selected="true">yes (default)</option> |
| 259 <option value="0">no</option> | |
| 260 <option value="2">only for high-quality alignments</option> | |
| 261 </param> | |
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262 <param name="microexon_spliceprob" type="float" value="" optional="true" label="Micro Exon splice probablility threshold" |
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263 help="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" > |
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264 <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/> |
| 0 | 265 </param> |
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266 <param name="prunelevel" type="select" label="Pruning level"> |
| 0 | 267 <option value="0">no pruning (default)</option> |
| 268 <option value="1">poor sequences</option> | |
| 269 <option value="2">repetitive sequences</option> | |
| 270 <option value="3">poor and repetitive sequences</option> | |
| 271 </param> | |
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272 <!-- could do this as a config file |
| 0 | 273 <param name="chrsubsetfile" type="data" format="fasta" label="User-supplied chromosome subset file" /> |
| 274 <param name="chrsubset" type="text" label="Chromosome subset to search" /> | |
| 275 --> | |
| 276 </when> | |
| 277 </conditional> | |
| 278 | |
| 279 <!-- Advanced Settings --> | |
| 280 <conditional name="advanced"> | |
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281 <param name="options" type="select" label="Advanced Settings" > |
| 0 | 282 <option value="default">Use default settings</option> |
| 283 <option value="used">Set Options</option> | |
| 284 </param> | |
| 285 <when value="default"/> | |
| 286 <when value="used"> | |
| 287 <param name="nolengths" type="boolean" checked="false" truevalue="--nolengths=true" falsevalue="" label="No intron lengths in alignment"/> | |
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288 <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" > |
| 0 | 289 <option value="">Don't invert the cDNA (default)</option> |
| 290 <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option> | |
| 291 <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option> | |
| 292 </param> | |
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293 <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)"> |
| 0 | 294 <validator type="in_range" message="introngap must be positive" min="0" /> |
| 295 </param> | |
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296 <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)"> |
| 0 | 297 <validator type="in_range" message="wraplength must be positive" min="1" /> |
| 298 </param> | |
| 299 <param name="npaths" type="integer" value="" optional="true" | |
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300 label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." > |
| 0 | 301 <validator type="in_range" message="npaths must be positive" min="0" /> |
| 302 </param> | |
| 303 <param name="suboptimal_score" type="integer" value="" optional="true" | |
| 304 label="Report only paths whose score is within this value of the best path" | |
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305 help="By default the program prints all paths found." > |
| 0 | 306 <validator type="in_range" message="suboptimal_score must be positive" min="0" /> |
| 307 </param> | |
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308 <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" > |
| 0 | 309 <validator type="in_range" message="chimera_overlap must be positive" min="0" /> |
| 310 </param> | |
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311 <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" |
| 0 | 312 label="Translates cDNA with corrections for frameshifts"/> |
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313 <param name="protein" type="select" label="Protein alignment" > |
| 0 | 314 <option value="">default</option> |
| 315 <option value="--fulllength=true">Assume full-length protein, starting with Met</option> | |
| 316 <option value="--truncate=true">Truncate alignment around full-length protein, Met to Stop</option> | |
| 317 </param> | |
| 318 </when> | |
| 319 </conditional> | |
| 320 | |
| 321 <!-- Output data --> | |
| 322 <conditional name="result"> | |
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323 <param name="format" type="select" label="Output" help="Select the output format" > |
| 0 | 324 <option value="gmap">GMAP default output</option> |
| 325 <option value="summary">Summary of alignments</option> | |
| 326 <option value="align">Alignment</option> | |
| 327 <option value="continuous">Alignment in three continuous lines</option> | |
| 328 <option value="continuous-by-exon">Alignment in three lines per exon</option> | |
| 329 <option value="compress">Print output in compressed format</option> | |
| 330 <option value="exons_dna">Print exons cDNA</option> | |
| 331 <option value="exons_gen">Print exons genomic</option> | |
| 332 <option value="protein_dna">Print protein sequence (cDNA)</option> | |
| 333 <option value="protein_gen">Print protein sequence (genomic)</option> | |
| 334 <option value="psl">PSL (BLAT) format</option> | |
| 335 <option value="gff3_gene">GFF3 gene format</option> | |
| 336 <option value="gff3_match_cdna">GFF3 match cDNA format</option> | |
| 337 <option value="gff3_match_est">GFF3 match EST format</option> | |
| 338 <option value="splicesites">splicesites output (for GSNAP)</option> | |
| 339 <option value="introns">introns output (for GSNAP)</option> | |
| 340 <option value="map_exons">IIT FASTA exon map format</option> | |
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341 <option value="map_ranges">IIT FASTA map format</option> |
| 0 | 342 <option value="coords">coords in table format</option> |
| 343 <option value="sam" selected="true">SAM format</option> | |
| 344 </param> | |
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345 <when value="gmap"/> |
| 0 | 346 <when value="summary"/> |
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347 <when value="align"/> |
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348 <when value="continuous"/> |
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349 <when value="continuous-by-exon"/> |
| 0 | 350 <when value="compress"/> |
| 351 <when value="exons_dna"/> | |
| 352 <when value="exons_gen"/> | |
| 353 <when value="protein_dna"/> | |
| 354 <when value="protein_gen"/> | |
| 355 <when value="psl"/> | |
| 356 <when value="gff3_gene"/> | |
| 357 <when value="gff3_match_cdna"/> | |
| 358 <when value="gff3_match_est"/> | |
| 359 <when value="splicesites"/> | |
| 360 <when value="introns"/> | |
| 361 <when value="map_exons"/> | |
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362 <when value="map_ranges"/> |
| 0 | 363 <when value="coords"/> |
| 364 <when value="sam"> | |
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365 <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads" help="The sampe option will generate SAM flags to indicate whether the read is the first or second end of a pair"/> |
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366 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print SAM headers (lines beginning with '@')"/> |
| 0 | 367 <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/> |
| 368 <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/> | |
| 369 <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/> | |
| 370 <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/> | |
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371 <param name="sam_use_0M" type="boolean" truevalue="--sam-use-0M" falsevalue="" checked="false" label="Insert 0M in CIGAR between adjacent insertions and deletions" help="Required by Picard, but can cause errors in other tools"/> |
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372 <param name="force_xs_dir" type="boolean" truevalue="--force-xs-dir" falsevalue="" checked="false" label="Force direction (disallow XS:A:?)" |
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373 help="For RNA-Seq alignments, disallows XS:A:? when the sense direction is unclear, and replaces this value arbitrarily with XS:A:+. May be useful for some programs, such as Cufflinks, that cannot handle XS:A:?. However, if you use this flag, the reported value of XS:A:+ in these cases will not be meaningful."/> |
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374 <param name="md_lowercase_snp" type="boolean" truevalue="--md-lowercase-snp" falsevalue="" checked="false" label="MD lowercase SNP" |
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375 help="In MD string, when known SNPs are given by the -v flag, prints difference nucleotides as lower-case when they, differ from reference but match a known alternate allele"/> |
| 0 | 376 </when> |
| 377 </conditional> <!-- name="result" --> | |
| 378 | |
| 379 <param name="split_output" type="boolean" truevalue="--split-output=gmap_out" falsevalue="" checked="false" label="Separate outputs for nomapping, uniq, mult, and chimera" help="(chimera only when chimera-margin is selected)"/> | |
| 380 | |
| 381 | |
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382 <!-- |
| 0 | 383 map=iitfile Map file. If argument is '?' (with the quotes), this lists available map files. |
| 384 mapexons Map each exon separately | |
| 385 mapboth Report hits from both strands of genome | |
| 386 flanking=INT Show flanking hits (default 0) | |
| 387 print-comment Show comment line for each hit | |
| 388 --> | |
| 389 | |
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390 <!-- |
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391 min-trimmed-coverage=FLOAT Do not print alignments with trimmed coverage less |
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392 this value (default=0.0, which means no filtering) |
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393 Note that chimeric alignments will be output regardless |
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394 of this filter |
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395 min-identity=FLOAT Do not print alignments with identity less |
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396 this value (default=0.0, which means no filtering) |
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397 Note that chimeric alignments will be output regardless |
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398 of this filter |
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399 --> |
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400 |
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401 |
| 0 | 402 |
| 403 </inputs> | |
| 404 <outputs> | |
| 405 <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/> | |
| 406 <data format="txt" name="output" label="${tool.name} on ${on_string} ${result.format}" > | |
| 407 <filter>(split_output == False)</filter> | |
| 408 <change_format> | |
| 409 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 410 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 411 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 412 <when input="result['format']" value="sam" format="sam"/> | |
| 413 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 414 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 415 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 416 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 417 </change_format> | |
| 418 </data> | |
| 419 <data format="txt" name="uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gmap_out.uniq"> | |
| 420 <filter>(split_output == True)</filter> | |
| 421 <change_format> | |
| 422 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 423 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 424 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 425 <when input="result['format']" value="sam" format="sam"/> | |
| 426 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 427 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 428 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 429 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 430 </change_format> | |
| 431 </data> | |
| 432 <data format="txt" name="transloc" label="${tool.name} on ${on_string} transloc.${result.format}" from_work_dir="gmap_out.transloc"> | |
| 433 <filter>(split_output == True)</filter> | |
| 434 <change_format> | |
| 435 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 436 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 437 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 438 <when input="result['format']" value="sam" format="sam"/> | |
| 439 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 440 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 441 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 442 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 443 </change_format> | |
| 444 </data> | |
| 445 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gmap_out.nomapping"> | |
| 446 <filter>(split_output == True)</filter> | |
| 447 <change_format> | |
| 448 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 449 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 450 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 451 <when input="result['format']" value="sam" format="sam"/> | |
| 452 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 453 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 454 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 455 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 456 </change_format> | |
| 457 </data> | |
| 458 <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}" from_work_dir="gmap_out.mult"> | |
| 459 <filter>(split_output == True)</filter> | |
| 460 <change_format> | |
| 461 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 462 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 463 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 464 <when input="result['format']" value="sam" format="sam"/> | |
| 465 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 466 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 467 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 468 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 469 </change_format> | |
| 470 </data> | |
| 471 </outputs> | |
| 472 <tests> | |
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473 <test> |
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474 <!-- |
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475 mimic first test from GMAP source code, mapping Human ERBB2 onto fragment of chr17 |
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476 $ gmap -A -g ss.chr17test ss.her2 |
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477 --> |
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478 <param name="input" value="ss.her2.fasta" ftype="fasta"/> |
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479 <!-- <param name="quality_protocol" value=""/> --> |
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480 <param name="genomeSource" value="history"/> |
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481 <param name="ownFile" value="ss.chr17.fasta" ftype="fasta"/> |
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482 <param name="format" value="align"/> |
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483 <param name="computation" value="default"/> |
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484 <param name="options" value="default"/> |
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485 <output name="output" file="ss.her2.chr17.txt" ftype="txt"/> |
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486 </test> |
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487 </tests> |
| 0 | 488 |
| 489 <help> | |
| 490 | |
| 491 **What it does** | |
| 492 | |
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493 GMAP (Genomic Mapping and Alignment Program) |
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494 |
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495 The functionality provided by gmap allows a user to: |
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497 1. map and align a single cDNA interactively against a large genome in |
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498 about a second, without the startup time of several minutes typically |
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499 needed by existing mapping programs; |
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500 2. switch arbitrarily among different genomes, without the need for a |
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501 preloaded server dedicated to each genome; |
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502 3. run the program on computers with as little as 128 MB of RAM (random |
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503 access memory) |
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504 4. perform high-throughput batch processing of cDNAs by using memory |
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505 mapping and multithreading when appropriate memory and hardware are |
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506 available; |
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507 5. generate accurate gene models, even in the presence of substantial |
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508 polymorphisms and sequence errors; |
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509 6. locate splice sites accurately without the use of probabilistic splice |
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510 site models, allowing generalized use of the program across species; |
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511 7. detect statistically significant microexons and incorporate them into |
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512 the alignment; and |
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513 8. handle mapping and alignment tasks on genomes having alternate |
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514 assemblies, linkage groups or strains. |
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516 It is developed by Thomas D. Wu of Genentech, Inc. |
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| 518 ------ | |
| 519 | |
| 520 **Know what you are doing** | |
| 521 | |
| 522 .. class:: warningmark | |
| 523 | |
| 524 You will want to read the README_ | |
| 525 | |
| 526 .. _README: http://research-pub.gene.com/gmap/src/README | |
| 527 </help> | |
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528 <citations> |
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529 <citation type="doi">10.1093/bioinformatics/bti310</citation> |
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530 </citations> |
| 0 | 531 </tool> |
| 532 |