Mercurial > repos > jjohnson > gmap
annotate gmap.xml @ 2:f6ba0f12cca2 draft
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
| author | peterjc |
|---|---|
| date | Wed, 28 Sep 2016 10:43:44 -0400 |
| parents | 74391fc6e3f2 |
| children | 488e9d642566 |
| rev | line source |
|---|---|
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
parents:
1
diff
changeset
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1 <tool id="gmap" name="GMAP" version="3.0.0"> |
| 0 | 2 <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description> |
| 3 <requirements> | |
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Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
parents:
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changeset
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4 <requirement type="package" version="2013-05-09">gmap</requirement> |
| 0 | 5 </requirements> |
| 6 <version_string>gmap --version</version_string> | |
| 7 <command> | |
| 8 #import os,os.path | |
| 9 gmap | |
| 10 --nthreads=4 --ordered | |
| 11 #if $refGenomeSource.genomeSource == "history": | |
| 12 --gseg=$refGenomeSource.ownFile | |
| 13 #elif $refGenomeSource.genomeSource == "gmapdb": | |
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Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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14 --dir=$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=$refGenomeSource.kmer | |
| 17 #end if | |
| 18 #else: | |
| 19 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) | |
| 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 | |
| 44 $result.no_sam_headers | |
|
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45 $result.sam_use_0M |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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46 $result.force_xs_dir |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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47 $result.md_lowercase_snp |
| 0 | 48 #* Removed in gmap version 2011-11-30 |
| 49 #if len($result.noncanonical_splices.__str__) > 0 | |
| 50 --noncanonical-splices=$result.noncanonical_splices | |
| 51 #end if | |
| 52 *# | |
| 53 #if len($result.read_group_id.__str__) > 0 | |
| 54 --read-group-id=$result.read_group_id | |
| 55 #end if | |
| 56 #if len($result.read_group_name.__str__) > 0 | |
| 57 --read-group-name=$result.read_group_name | |
| 58 #end if | |
| 59 #if len($result.read_group_library.__str__) > 0 | |
| 60 --read-group-library=$result.read_group_library | |
| 61 #end if | |
| 62 #if len($result.read_group_platform.__str__) > 0 | |
| 63 --read-group-platform=$result.read_group_platform | |
| 64 #end if | |
| 65 #elif $result.format != "gmap": | |
| 66 --format=$result.format | |
| 67 #end if | |
| 68 #if $computation.options == "advanced": | |
| 69 $computation.nosplicing | |
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70 $computation.find_shifted_canonical |
| 0 | 71 $computation.cross_species |
| 72 #if len($computation.min_intronlength.__str__) > 0 | |
| 73 --min-intronlength=$computation.min_intronlength | |
| 74 #end if | |
| 75 #if len($computation.intronlength.__str__) > 0 | |
| 76 --intronlength=$computation.intronlength | |
| 77 #end if | |
| 78 #if len($computation.localsplicedist.__str__) > 0 | |
| 79 --localsplicedist=$computation.localsplicedist | |
| 80 #end if | |
| 81 #if len($computation.totallength.__str__) > 0 | |
| 82 --totallength=$computation.totallength | |
| 83 #end if | |
| 84 #if len($computation.trimendexons.__str__) > 0 | |
| 85 --trimendexons=$computation.trimendexons | |
| 86 #end if | |
| 87 --direction=$computation.direction | |
| 88 --canonical-mode=$computation.canonical | |
| 89 --prunelevel=$computation.prunelevel | |
| 90 --allow-close-indels=$computation.allow_close_indels | |
| 91 #if len($computation.microexon_spliceprob.__str__) >= 0: | |
| 92 --microexon-spliceprob=$computation.microexon_spliceprob | |
| 93 #end if | |
| 94 #if len($computation.chimera_margin.__str__) >= 0: | |
| 95 --chimera-margin=$computation.chimera_margin | |
| 96 #end if | |
| 97 #end if | |
| 98 #if $advanced.options == "used": | |
| 99 #if len($advanced.npaths.__str__) > 0: | |
| 100 --npaths=$advanced.npaths | |
| 101 #end if | |
| 102 #if len($advanced.suboptimal_score.__str__) > 0: | |
| 103 --suboptimal-score=$advanced.suboptimal_score | |
| 104 #end if | |
| 105 #if len($advanced.chimera_overlap.__str__) > 0: | |
| 106 --chimera_overlap=$advanced.chimera_overlap | |
| 107 #end if | |
| 108 $advanced.protein | |
| 109 $advanced.tolerant | |
| 110 $advanced.nolengths | |
| 111 $advanced.invertmode | |
| 112 #if len($advanced.introngap.__str__) > 0: | |
| 113 --introngap=$advanced.introngap | |
| 114 #end if | |
| 115 #if len($advanced.wraplength.__str__) > 0: | |
| 116 --wraplength=$advanced.wraplength | |
| 117 #end if | |
| 118 #end if | |
| 119 #if $split_output == True | |
| 120 $split_output | |
| 121 #end if | |
| 122 #if len($quality_protocol.__str__) > 0: | |
| 123 --quality-protocol=$quality_protocol | |
| 124 #end if | |
| 125 $input | |
| 126 #for $i in $inputs: | |
| 127 ${i.added_input} | |
| 128 #end for | |
| 129 #if $split_output == True | |
| 130 2> $gmap_stderr | |
| 131 #else | |
| 132 2> $gmap_stderr > $output | |
| 133 #end if | |
| 134 </command> | |
| 135 <inputs> | |
| 136 <!-- Input data --> | |
| 137 <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="<H2>Input Sequences</H2>Select an mRNA or EST dataset to map" /> | |
| 138 <repeat name="inputs" title="addtional mRNA or EST dataset to map"> | |
| 139 <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/> | |
| 140 </repeat> | |
| 141 <param name="quality_protocol" type="select" label="Protocol for input quality scores"> | |
| 142 <option value="">No quality scores</option> | |
| 143 <option value="sanger">Sanger quality scores</option> | |
| 144 <option value="illumina">Illumina quality scores</option> | |
| 145 </param> | |
| 146 | |
| 147 <!-- GMAPDB for mapping --> | |
| 148 <conditional name="refGenomeSource"> | |
| 149 <param name="genomeSource" type="select" label="<HR><H2>Map To</H2>Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> | |
| 150 <option value="indexed">Use a built-in index</option> | |
| 151 <option value="gmapdb">Use gmapdb from the history</option> | |
| 152 <option value="history">Use a fasta reference sequence from the history</option> | |
| 153 </param> | |
| 154 <when value="indexed"> | |
| 155 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> | |
| 156 <options from_file="gmap_indices.loc"> | |
| 157 <column name="uid" index="0" /> | |
| 158 <column name="dbkey" index="1" /> | |
| 159 <column name="name" index="2" /> | |
| 160 <column name="kmers" index="3" /> | |
| 161 <column name="maps" index="4" /> | |
| 162 <column name="snps" index="5" /> | |
| 163 <column name="value" index="6" /> | |
| 164 </options> | |
| 165 </param> | |
| 166 <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> | |
| 167 <options from_file="gmap_indices.loc"> | |
| 168 <column name="name" index="3"/> | |
| 169 <column name="value" index="3"/> | |
| 170 <filter type="param_value" ref="gmapindex" column="6"/> | |
| 171 <filter type="multiple_splitter" column="3" separator=","/> | |
| 172 <filter type="add_value" name="" value=""/> | |
| 173 <filter type="sort_by" column="3"/> | |
| 174 </options> | |
| 175 </param> | |
|
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
parents:
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176 <!-- |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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177 basesize=INT Base size to use in genome database. If not specified, the program |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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178 will find the highest available base size in the genome database |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
parents:
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179 within selected k-mer size |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
parents:
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180 sampling=INT Sampling to use in genome database. If not specified, the program |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
parents:
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181 will find the smallest available sampling value in the genome database |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
parents:
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diff
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182 within selected basesize and k-mer size |
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Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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183 |
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f6ba0f12cca2
Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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184 --> |
| 0 | 185 <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" help=""> |
| 186 <options from_file="gmap_indices.loc"> | |
| 187 <column name="name" index="4"/> | |
| 188 <column name="value" index="4"/> | |
| 189 <filter type="param_value" ref="gmapindex" column="6"/> | |
| 190 <filter type="multiple_splitter" column="4" separator=","/> | |
| 191 <filter type="add_value" name="" value=""/> | |
| 192 <filter type="sort_by" column="4"/> | |
| 193 </options> | |
| 194 </param> | |
| 195 </when> | |
| 196 <when value="gmapdb"> | |
| 197 <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" | |
| 198 help="A GMAP database built with GMAP Build"/> | |
| 199 <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> | |
| 200 <options> | |
| 201 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> | |
| 202 </options> | |
| 203 </param> | |
| 204 <param name="map" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> | |
| 205 <options> | |
| 206 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> | |
| 207 </options> | |
| 208 </param> | |
| 209 </when> | |
| 210 <when value="history"> | |
| 211 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" | |
| 212 help="Fasta containing genomic DNA sequence"/> | |
| 213 </when> | |
| 214 </conditional> | |
| 215 | |
| 216 | |
| 217 <!-- Computation options --> | |
| 218 <conditional name="computation"> | |
| 219 <param name="options" type="select" label="<HR>Computational Settings" help=""> | |
| 220 <option value="default">Use default settings</option> | |
| 221 <option value="advanced">Set Computation Options</option> | |
| 222 </param> | |
| 223 <when value="default"/> | |
| 224 <when value="advanced"> | |
| 225 <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/> | |
| 226 <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." > | |
| 227 <validator type="in_range" message="min_intronlength must be positive" min="0" /> | |
| 228 </param> | |
| 229 <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" > | |
| 230 <validator type="in_range" message="intronlength must be positive" min="0" /> | |
| 231 </param> | |
| 232 <param name="localsplicedist" type="integer" value="" optional="true" label="Max length for known splice sites at ends of sequence (default 200000)" > | |
| 233 <validator type="in_range" message="localsplicedist must be positive" min="0" /> | |
| 234 </param> | |
| 235 <param name="totallength" type="integer" value="" optional="true" label="Max total intron length (default 2400000)" > | |
| 236 <validator type="in_range" message="totallength must be positive" min="0" /> | |
| 237 </param> | |
| 238 <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera" | |
|
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239 help=" default is 40, To turn off, set to 0" > |
| 0 | 240 <validator type="in_range" message="chimera_margin must be positive" min="0" /> |
| 241 </param> | |
| 242 <param name="direction" type="select" label="cDNA direction"> | |
| 243 <option value="auto">auto</option> | |
| 244 <option value="sense_force">sense_force</option> | |
| 245 <option value="antisense_force">antisense_force</option> | |
| 246 <option value="sense_filter">sense_filter</option> | |
| 247 <option value="antisense_filter">antisense_filter</option> | |
| 248 </param> | |
| 249 <param name="trimendexons" type="integer" value="" optional="true" label="Trim end exons with fewer than given number of matches (in nt, default 12)" > | |
| 250 <validator type="in_range" message="trimendexons must be positive" min="1" /> | |
| 251 </param> | |
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Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
peterjc
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252 <param name="find_shifted_canonical" type="boolean" truevalue="--find-shifted-canonical-species" falsevalue="" checked="false" label="find-shifted-canonical Use a more sensitive search for canonical splicing" help=""/> |
| 0 | 253 <param name="cross_species" type="boolean" truevalue="--cross-species" falsevalue="" checked="false" label="Cross-species alignment" help="For cross-species alignments, use a more sensitive search for canonical splicing"/> |
| 254 | |
| 255 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns"> | |
| 256 <option value="1">high reward (default)</option> | |
| 257 <option value="0">low reward</option> | |
| 258 <option value="2">low reward for high-identity sequences</option> | |
| 259 </param> | |
| 260 <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other"> | |
| 261 <option value="1" selected="true">yes (default)</option> | |
| 262 <option value="0">no</option> | |
| 263 <option value="2">only for high-quality alignments</option> | |
| 264 </param> | |
| 265 <param name="microexon_spliceprob" type="float" value="" optional="true" label="Micro Exon splice probablility threshold" | |
| 266 help="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" > | |
| 267 <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/> | |
| 268 </param> | |
| 269 <param name="prunelevel" type="select" label="Pruning level"> | |
| 270 <option value="0">no pruning (default)</option> | |
| 271 <option value="1">poor sequences</option> | |
| 272 <option value="2">repetitive sequences</option> | |
| 273 <option value="3">poor and repetitive sequences</option> | |
| 274 </param> | |
| 275 <!-- could do this as a config file | |
| 276 <param name="chrsubsetfile" type="data" format="fasta" label="User-supplied chromosome subset file" /> | |
| 277 <param name="chrsubset" type="text" label="Chromosome subset to search" /> | |
| 278 --> | |
| 279 </when> | |
| 280 </conditional> | |
| 281 | |
| 282 <!-- Advanced Settings --> | |
| 283 <conditional name="advanced"> | |
| 284 <param name="options" type="select" label="<HR>Advanced Settings" help=""> | |
| 285 <option value="default">Use default settings</option> | |
| 286 <option value="used">Set Options</option> | |
| 287 </param> | |
| 288 <when value="default"/> | |
| 289 <when value="used"> | |
| 290 <param name="nolengths" type="boolean" checked="false" truevalue="--nolengths=true" falsevalue="" label="No intron lengths in alignment"/> | |
| 291 <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help=""> | |
| 292 <option value="">Don't invert the cDNA (default)</option> | |
| 293 <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option> | |
| 294 <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option> | |
| 295 </param> | |
| 296 <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)"> | |
| 297 <validator type="in_range" message="introngap must be positive" min="0" /> | |
| 298 </param> | |
| 299 <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)"> | |
| 300 <validator type="in_range" message="wraplength must be positive" min="1" /> | |
| 301 </param> | |
| 302 <param name="npaths" type="integer" value="" optional="true" | |
| 303 label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." > | |
| 304 <validator type="in_range" message="npaths must be positive" min="0" /> | |
| 305 </param> | |
| 306 <param name="suboptimal_score" type="integer" value="" optional="true" | |
| 307 label="Report only paths whose score is within this value of the best path" | |
| 308 help="By default the program prints all paths found." > | |
| 309 <validator type="in_range" message="suboptimal_score must be positive" min="0" /> | |
| 310 </param> | |
| 311 <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" > | |
| 312 <validator type="in_range" message="chimera_overlap must be positive" min="0" /> | |
| 313 </param> | |
| 314 <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" | |
| 315 label="Translates cDNA with corrections for frameshifts"/> | |
| 316 <param name="protein" type="select" label="Protein alignment" help=""> | |
| 317 <option value="">default</option> | |
| 318 <option value="--fulllength=true">Assume full-length protein, starting with Met</option> | |
| 319 <option value="--truncate=true">Truncate alignment around full-length protein, Met to Stop</option> | |
| 320 </param> | |
| 321 </when> | |
| 322 </conditional> | |
| 323 | |
| 324 <!-- Output data --> | |
| 325 <conditional name="result"> | |
| 326 <param name="format" type="select" label="<HR><H2>Output</H2>Select the output format" help=""> | |
| 327 <option value="gmap">GMAP default output</option> | |
| 328 <option value="summary">Summary of alignments</option> | |
| 329 <option value="align">Alignment</option> | |
| 330 <option value="continuous">Alignment in three continuous lines</option> | |
| 331 <option value="continuous-by-exon">Alignment in three lines per exon</option> | |
| 332 <option value="compress">Print output in compressed format</option> | |
| 333 <option value="exons_dna">Print exons cDNA</option> | |
| 334 <option value="exons_gen">Print exons genomic</option> | |
| 335 <option value="protein_dna">Print protein sequence (cDNA)</option> | |
| 336 <option value="protein_gen">Print protein sequence (genomic)</option> | |
| 337 <option value="psl">PSL (BLAT) format</option> | |
| 338 <option value="gff3_gene">GFF3 gene format</option> | |
| 339 <option value="gff3_match_cdna">GFF3 match cDNA format</option> | |
| 340 <option value="gff3_match_est">GFF3 match EST format</option> | |
| 341 <option value="splicesites">splicesites output (for GSNAP)</option> | |
| 342 <option value="introns">introns output (for GSNAP)</option> | |
| 343 <option value="map_exons">IIT FASTA exon map format</option> | |
|
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Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013
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344 <option value="map_ranges">IIT FASTA map format</option> |
| 0 | 345 <option value="coords">coords in table format</option> |
| 346 <option value="sam" selected="true">SAM format</option> | |
| 347 </param> | |
| 348 <when value="gmap"> | |
| 349 </when> | |
| 350 <when value="summary"/> | |
| 351 <when value="align"> | |
| 352 </when> | |
| 353 <when value="continuous"> | |
| 354 </when> | |
| 355 <when value="continuous-by-exon"> | |
| 356 </when> | |
| 357 <when value="compress"/> | |
| 358 <when value="exons_dna"/> | |
| 359 <when value="exons_gen"/> | |
| 360 <when value="protein_dna"/> | |
| 361 <when value="protein_gen"/> | |
| 362 <when value="psl"/> | |
| 363 <when value="gff3_gene"/> | |
| 364 <when value="gff3_match_cdna"/> | |
| 365 <when value="gff3_match_est"/> | |
| 366 <when value="splicesites"/> | |
| 367 <when value="introns"/> | |
| 368 <when value="map_exons"/> | |
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369 <when value="map_ranges"/> |
| 0 | 370 <when value="coords"/> |
| 371 <when value="sam"> | |
| 372 <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/> | |
| 373 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> | |
| 374 <!-- Removed in gmap version 2011-11-30 | |
| 375 <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING."> | |
| 376 <option value="">Use default</option> | |
| 377 <option value="N">N</option> | |
| 378 <option value="D">D</option> | |
| 379 </param> | |
| 380 --> | |
| 381 <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/> | |
| 382 <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/> | |
| 383 <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/> | |
| 384 <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/> | |
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385 <param name="sam_use_0M" type="boolean" truevalue="--sam-use-0M" falsevalue="" checked="false" label="Insert 0M in CIGAR between adjacent insertions and deletions" help="Required by Picard, but can cause errors in other tools"/> |
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386 <param name="force_xs_dir" type="boolean" truevalue="--force-xs-dir" falsevalue="" checked="false" label="Force direction (disallow XS:A:?)" |
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387 help="For RNA-Seq alignments, disallows XS:A:? when the sense direction is unclear, and replaces this value arbitrarily with XS:A:+. May be useful for some programs, such as Cufflinks, that cannot handle XS:A:?. However, if you use this flag, the reported value of XS:A:+ in these cases will not be meaningful."/> |
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388 <param name="md_lowercase_snp" type="boolean" truevalue="--md-lowercase-snp" falsevalue="" checked="false" label="MD lowercase SNP" |
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389 help="In MD string, when known SNPs are given by the -v flag, prints difference nucleotides as lower-case when they, differ from reference but match a known alternate allele"/> |
| 0 | 390 </when> |
| 391 </conditional> <!-- name="result" --> | |
| 392 | |
| 393 <param name="split_output" type="boolean" truevalue="--split-output=gmap_out" falsevalue="" checked="false" label="Separate outputs for nomapping, uniq, mult, and chimera" help="(chimera only when chimera-margin is selected)"/> | |
| 394 | |
| 395 | |
| 396 <!-- | |
| 397 map=iitfile Map file. If argument is '?' (with the quotes), this lists available map files. | |
| 398 mapexons Map each exon separately | |
| 399 mapboth Report hits from both strands of genome | |
| 400 flanking=INT Show flanking hits (default 0) | |
| 401 print-comment Show comment line for each hit | |
| 402 --> | |
| 403 | |
|
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404 <!-- |
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405 min-trimmed-coverage=FLOAT Do not print alignments with trimmed coverage less |
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406 this value (default=0.0, which means no filtering) |
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407 Note that chimeric alignments will be output regardless |
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408 of this filter |
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409 min-identity=FLOAT Do not print alignments with identity less |
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410 this value (default=0.0, which means no filtering) |
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411 Note that chimeric alignments will be output regardless |
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412 of this filter |
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413 --> |
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414 |
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415 |
| 0 | 416 |
| 417 </inputs> | |
| 418 <outputs> | |
| 419 <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/> | |
| 420 <data format="txt" name="output" label="${tool.name} on ${on_string} ${result.format}" > | |
| 421 <filter>(split_output == False)</filter> | |
| 422 <change_format> | |
| 423 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 424 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 425 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 426 <when input="result['format']" value="sam" format="sam"/> | |
| 427 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 428 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 429 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 430 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 431 </change_format> | |
| 432 </data> | |
| 433 <data format="txt" name="uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gmap_out.uniq"> | |
| 434 <filter>(split_output == True)</filter> | |
| 435 <change_format> | |
| 436 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 437 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 438 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 439 <when input="result['format']" value="sam" format="sam"/> | |
| 440 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 441 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 442 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 443 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 444 </change_format> | |
| 445 </data> | |
| 446 <data format="txt" name="transloc" label="${tool.name} on ${on_string} transloc.${result.format}" from_work_dir="gmap_out.transloc"> | |
| 447 <filter>(split_output == True)</filter> | |
| 448 <change_format> | |
| 449 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 450 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 451 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 452 <when input="result['format']" value="sam" format="sam"/> | |
| 453 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 454 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 455 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 456 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 457 </change_format> | |
| 458 </data> | |
| 459 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gmap_out.nomapping"> | |
| 460 <filter>(split_output == True)</filter> | |
| 461 <change_format> | |
| 462 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 463 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 464 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 465 <when input="result['format']" value="sam" format="sam"/> | |
| 466 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 467 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 468 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 469 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 470 </change_format> | |
| 471 </data> | |
| 472 <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}" from_work_dir="gmap_out.mult"> | |
| 473 <filter>(split_output == True)</filter> | |
| 474 <change_format> | |
| 475 <when input="result['format']" value="gff3_gene" format="gff3"/> | |
| 476 <when input="result['format']" value="gff3_match_cdna" format="gff3"/> | |
| 477 <when input="result['format']" value="gff3_match_est" format="gff3"/> | |
| 478 <when input="result['format']" value="sam" format="sam"/> | |
| 479 <when input="result['format']" value="splicesites" format="gmap_splicesites"/> | |
| 480 <when input="result['format']" value="introns" format="gmap_introns"/> | |
| 481 <when input="result['format']" value="map_genes" format="gmap_annotation"/> | |
| 482 <when input="result['format']" value="map_exons" format="gmap_annotation"/> | |
| 483 </change_format> | |
| 484 </data> | |
| 485 </outputs> | |
| 486 <tests> | |
| 487 </tests> | |
| 488 | |
| 489 <help> | |
| 490 | |
| 491 **What it does** | |
| 492 | |
| 493 GMAP_ (Genomic Mapping and Alignment Program) The functionality provided by gmap allows a user to: (1) map and align a single cDNA interactively against a large genome in about a second, without the startup time of several minutes typically needed by existing mapping programs; (2) switch arbitrarily among different genomes, without the need for a preloaded server dedicated to each genome; (3) run the program on computers with as little as 128 MB of RAM (random access memory); (4) perform high-throughput batch processing of cDNAs by using memory mapping and multithreading when appropriate memory and hardware are available; (5) generate accurate gene models, even in the presence of substantial polymorphisms and sequence errors; (6) locate splice sites accurately without the use of probabilistic splice site models, allowing generalized use of the program across species; (7) detect statistically significant microexons and incorporate them into the alignment; and (8) handle mapping and alignment tasks on genomes having alternate assemblies, linkage groups or strains. It is developed by Thomas D. Wu of Genentech, Inc. | |
| 494 | |
| 495 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 | |
| 496 | |
| 497 .. _GMAP: http://research-pub.gene.com/gmap/ | |
| 498 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 | |
| 499 | |
| 500 ------ | |
| 501 | |
| 502 **Know what you are doing** | |
| 503 | |
| 504 .. class:: warningmark | |
| 505 | |
| 506 You will want to read the README_ | |
| 507 | |
| 508 .. _README: http://research-pub.gene.com/gmap/src/README | |
| 509 | |
| 510 </help> | |
| 511 </tool> | |
| 512 |