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| author | nml |
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| date | Wed, 25 Oct 2017 12:03:56 -0400 |
| parents | 599a4dc309aa |
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1 <tool id="srst2" name="SRST2" version="0.3.7"> |
| 0 | 2 <description>Short Read Sequence Typing for Bacterial Pathogens</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.1.4.6">srst2</requirement> | |
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5 <requirement type="package" version="08-07-2014">vfdb</requirement> |
| 0 | 6 </requirements> |
| 7 <stdio> | |
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8 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> |
| 0 | 9 </stdio> |
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10 <command><![CDATA[ |
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11 $__tool_directory__/srst2.pl $bam_results $scores $pileup |
| 0 | 12 |
| 13 #if $mlst_or_genedb.job_type == "mlst_only" | |
| 14 m $txt_results $alleles | |
| 15 #if ($mlst_or_genedb.allele_choice.allele_report=="all") | |
| 16 all | |
| 17 #else if ($mlst_or_genedb.allele_choice.allele_report=="new") | |
| 18 new | |
| 19 #end if | |
| 20 #else if $mlst_or_genedb.job_type == "custom_only" | |
| 21 g $genes_results $fullgenes_results | |
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22 #* |
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23 to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed |
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24 make the database names an array and then join |
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25 *# |
| 0 | 26 #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )]) |
| 27 "$dbs" | |
| 28 #else if $mlst_or_genedb.job_type == "vfdb_only" | |
| 29 g $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name | |
| 30 #else if $mlst_or_genedb.job_type == "mlst_custom" | |
| 31 b $txt_results $genes_results $fullgenes_results | |
| 32 #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )]) | |
| 33 "$dbs" | |
| 34 #else if $mlst_or_genedb.job_type == "mlst_vfdb" | |
| 35 b $txt_results $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name | |
| 36 #end if | |
| 37 | |
| 38 #if $single_or_paired.type == "single" | |
| 39 "$single_or_paired.input_se.element_identifier" | |
| 40 --input_se "$input_se" | |
| 41 #elif $single_or_paired.type == "paired" | |
| 42 "$single_or_paired.forward_pe.name" | |
| 43 --input_pe "$single_or_paired.forward_pe" "$single_or_paired.reverse_pe" | |
| 44 #else | |
| 45 "$single_or_paired.fastq_collection.forward.name" | |
| 46 --input_pe "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.reverse" | |
| 47 #end if | |
| 48 | |
| 49 #if ($mlst_or_genedb.job_type=="mlst_only") | |
| 50 --mlst_db $mlst_db | |
| 51 --mlst_definition $mlst_defs | |
| 52 --mlst_delimiter "'$mlst_or_genedb.mlst_delim'" | |
| 53 --mlst_max_mismatch $mlst_or_genedb.mlst_max_mismatch | |
| 54 --report_all_consensus | |
| 55 #else if ($mlst_or_genedb.job_type=="mlst_vfdb") | |
| 56 --mlst_db $mlst_db | |
| 57 --mlst_definition $mlst_defs | |
| 58 --mlst_delimiter "'$mlst_or_genedb.mlst_delim'" | |
| 59 --mlst_max_mismatch $mlst_or_genedb.mlst_max_mismatch | |
| 60 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
| 61 --gene_db \$VF_PATH/${mlst_or_genedb.vfdb_in.fields.path} | |
| 62 #else if ($mlst_or_genedb.job_type=="mlst_custom") | |
| 63 --gene_db | |
| 64 #for $i, $database in enumerate( $mlst_or_genedb.databases ) | |
| 65 $database.gene_db | |
| 66 #end for | |
| 67 --mlst_db $mlst_db | |
| 68 --mlst_delimiter "'$mlst_or_genedb.mlst_delim'" | |
| 69 --mlst_max_mismatch $mlst_or_genedb.mlst_max_mismatch | |
| 70 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
| 71 --mlst_definition $mlst_defs | |
| 72 #else if ($mlst_or_genedb.job_type=="vfdb_only") | |
| 73 --gene_db \$VF_PATH/${mlst_or_genedb.vfdb_in.fields.path} | |
| 74 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
| 75 #else if ($mlst_or_genedb.job_type=="custom_only") | |
| 76 --gene_db | |
| 77 #for $i, $database in enumerate( $mlst_or_genedb.databases ) | |
| 78 $database.gene_db | |
| 79 #end for | |
| 80 --gene_max_mismatch $mlst_or_genedb.gene_max_mismatch | |
| 81 #end if | |
| 82 | |
| 83 --read_type q | |
| 84 | |
| 85 --save_scores | |
| 86 | |
| 87 #if $options.select == "advanced" | |
| 88 #if $options.min_coverage | |
| 89 --min_coverage $options.min_coverage | |
| 90 #end if | |
| 91 #if $options.max_divergence | |
| 92 --max_divergence $options.max_divergence | |
| 93 #end if | |
| 94 #if $options.min_depth | |
| 95 --min_depth $options.min_depth | |
| 96 #end if | |
| 97 #if $options.min_edge_depth | |
| 98 --min_edge_depth $options.min_edge_depth | |
| 99 #end if | |
| 100 #if $options.prob_err | |
| 101 --prob_err $options.prob_err | |
| 102 #end if | |
| 103 #if $options.stop_after | |
| 104 --stop_after $options.stop_after | |
| 105 #end if | |
| 106 --other "'-p \${GALAXY_SLOTS:-1} | |
| 107 #if $options.maxins | |
| 108 --maxins $options.maxins | |
| 109 --minins $options.minins | |
| 110 #end if | |
| 111 '" | |
| 112 #if $options.mapq | |
| 113 --mapq $options.mapq | |
| 114 #end if | |
| 115 #if $options.baseq | |
| 116 --baseq $options.baseq | |
| 117 #end if | |
| 118 #else | |
| 119 --other "'-p \${GALAXY_SLOTS:-1}'" | |
| 120 #end if | |
| 121 | |
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122 --output \${PWD}/out |
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123 ]]></command> |
| 0 | 124 <inputs> |
| 125 <conditional name="single_or_paired"> | |
| 126 <param name="type" type="select" label="Read type"> | |
| 127 <option value="single">Single-end</option> | |
| 128 <option value="paired">Paired-end</option> | |
| 129 <option value="collection">Collection Paired-end</option> | |
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130 </param> |
| 0 | 131 <when value="single"> |
| 132 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/> | |
| 133 </when> | |
| 134 <when value="paired"> | |
| 135 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/> | |
| 136 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/> | |
| 137 </when> | |
| 138 <when value="collection"> | |
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139 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" /> |
| 0 | 140 </when> |
| 141 </conditional> | |
| 142 | |
| 143 <conditional name="mlst_or_genedb"> | |
| 144 <param name="job_type" type="select" label="Job type"> | |
| 145 <option value="mlst_only">MLST only</option> | |
| 146 <option value="mlst_vfdb">MLST and VFDB</option> | |
| 147 <option value="mlst_custom">MLST and custom database</option> | |
| 148 <option value="vfdb_only">VFDB only</option> | |
| 149 <option value="custom_only">Custom database only</option> | |
| 150 </param> | |
| 151 <when value="mlst_only"> | |
| 152 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> | |
| 153 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> | |
| 154 <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
| 155 <conditional name="allele_choice"> | |
| 156 <param name="allele_report" type="select" label="Reported Alleles" > | |
| 157 <option value="all">All</option> | |
| 158 <option value="new">Only New</option> | |
| 159 </param> | |
| 160 <when value="all"/> | |
| 161 <when value="new"/> | |
| 162 </conditional> | |
| 163 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > | |
| 164 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> | |
| 165 </param> | |
| 166 </when> | |
| 167 <when value="mlst_vfdb"> | |
| 168 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> | |
| 169 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> | |
| 170 <param name="vfdb_in" type="select" label="Choose a VFDB strain"> | |
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171 <options from_data_table="vfdb_fasta_files" /> |
| 0 | 172 </param> |
| 173 <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
| 174 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
| 175 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > | |
| 176 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> | |
| 177 </param> | |
| 178 </when> | |
| 179 <when value="mlst_custom"> | |
| 180 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> | |
| 181 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> | |
| 182 <repeat name="databases" title="Databases" min="1"> | |
| 183 <param name="gene_db" type="data" format="fasta" label="Fasta file for gene database" /> | |
| 184 </repeat> | |
| 185 <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
| 186 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
| 187 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > | |
| 188 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> | |
| 189 </param> | |
| 190 </when> | |
| 191 <when value="vfdb_only"> | |
| 192 <param name="vfdb_in" type="select" label="Choose a VFDB strain"> | |
| 193 <options from_data_table="vfdb_fasta_files" > | |
| 194 <filter type="sort_by" column="2" /> | |
| 195 <validator type="no_options" message="No strains are available" /> | |
| 196 </options> | |
| 197 </param> | |
| 198 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
| 199 </when> | |
| 200 <when value="custom_only"> | |
| 201 <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> | |
| 202 <repeat name="databases" title="Databases" min="1"> | |
| 203 <param name="gene_db" type="data" format="fasta" label="Fasta file for gene database" /> | |
| 204 </repeat> | |
| 205 </when> | |
| 206 </conditional> | |
| 207 <conditional name="options"> | |
| 208 <param name="select" type="select" label="Options Type"> | |
| 209 <option value="basic">Basic</option> | |
| 210 <option value="advanced">Advanced</option> | |
| 211 </param> | |
| 212 <when value="advanced"> | |
| 213 <param name="min_coverage" type="integer" label="Minimum %coverage cutoff for gene reporting" value="90"/> | |
| 214 <param name="max_divergence" type="integer" label="Maximum %divergence cutoff for gene reporting" value="10"/> | |
| 215 <param name="min_depth" type="integer" label="Minimum mean depth to flag as dubious allele call" value="5"/> | |
| 216 <param name="min_edge_depth" type="integer" label="Minimum edge depth to flag as dubious allele call" value="2"/> | |
| 217 <param name="prob_err" type="float" label="Probability of sequencing error" value="0.01"/> | |
| 218 <param name="stop_after" type="integer" label="Stop mapping after this number of reads have been mapped (otherwise map all)" optional="true"/> | |
| 219 <param name="mapq" type="integer" label="Samtools -q parameter" value="1"/> | |
| 220 <param name="baseq" type="integer" label="Samtools -Q parameter" value="20"/> | |
| 221 <param name="minins" type="integer" label="Bowtie 2 -I parameter. The minimum fragment length for valid paired-end alignments." value="0" > | |
| 222 <validator type="in_range" message="Must be less than -X parameter." min="0"/> | |
| 223 </param> | |
| 224 <param name="maxins" type="integer" label="Bowtie 2 -X parameter. The maximum fragment length for valid paired-end alignments." value="1000" > | |
| 225 <validator type="in_range" message="Must be greater than -I parameter." min="0"/> | |
| 226 </param> | |
| 227 | |
| 228 </when> | |
| 229 <when value="basic"/> | |
| 230 </conditional> | |
| 231 </inputs> | |
| 232 | |
| 233 <outputs> | |
| 234 <data format="bam" name="bam_results" label="Bam Results"/> | |
| 235 <data format="tabular" name="scores" label="Scores"/> | |
| 236 <data format="tabular" name="pileup" label="Pileup"/> | |
| 237 <data format="fasta" name="alleles" label="Alleles"> | |
| 238 <filter>mlst_or_genedb['job_type']=="mlst_only"</filter> | |
| 239 </data> | |
| 240 <data format="tabular" name="txt_results" label="Text Results" > | |
| 241 <filter>mlst_or_genedb['job_type']!="vfdb_only"</filter> | |
| 242 <filter>mlst_or_genedb['job_type']!="custom_only"</filter> | |
| 243 </data> | |
| 244 <data format="tabular" name="genes_results" label="Genes Results" > | |
| 245 <filter>mlst_or_genedb['job_type']!="mlst_only"</filter> | |
| 246 </data> | |
| 247 <data format="tabular" name="fullgenes_results" label="Full Genes Results" > | |
| 248 <filter>mlst_or_genedb['job_type']!= "mlst_only"</filter> | |
| 249 </data> | |
| 250 </outputs> | |
| 251 | |
| 252 <tests> | |
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253 <test> |
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254 <param name="type" value="collection" /> |
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255 <param name="fastq_collection"> |
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256 <collection type="paired"> |
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257 <element name="forward" value="ERR028678_sampled_1.fastq" /> |
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258 <element name="reverse" value="ERR028678_sampled_2.fastq" /> |
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259 </collection> |
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260 </param> |
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261 <param name="job_type" value="mlst_only" /> |
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262 <param name="mlst_defs" value="ecoli.txt" /> |
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263 <param name="mlst_db" value="Escherichia_coli#1.fasta" /> |
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264 <param name="mlst_max_mismatch" value="10" /> |
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265 <param name="mlst_delim" value="-" /> |
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266 <output name="bam_results" file="ERR028678_sampled.bam" ftype="bam" lines_diff="2" /> |
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267 <output name="scores" file="ERR028678_sampled_scores.tabular" /> |
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268 <!-- Don't test pileup as it is too large of a file > 90 MB --> |
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269 <!-- <output name="pileup" file="ERR028678_sampled_pileup.tabular" />--> |
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270 <output name="alleles" file="ERR028678_sampled_alleles.fasta" /> |
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271 <output name="txt_results" file="ERR028678_sampled_text_results.tabular" /> |
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272 </test> |
| 0 | 273 </tests> |
| 274 | |
| 275 | |
| 276 <help> | |
| 277 What it does | |
| 278 ============ | |
| 279 | |
| 280 Short Read Sequence Typing for Bacterial Pathogens | |
| 281 | |
| 282 This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. The tool has a database of virulence factors that was extracted from http://www.mgc.ac.cn/VFs/ . | |
| 283 | |
| 284 For more information about SRST2 and for instructions on how to format custom databases, visit https://github.com/katholt/srst2 | |
| 285 | |
| 286 | |
| 287 Usage | |
| 288 ===== | |
| 289 | |
| 290 Basic Options | |
| 291 ------------- | |
| 292 | |
| 293 **Read Type** | |
| 294 - Single-end: Single end read file(s) for analysing (--input_se) | |
| 295 - Paired-end: Paired end read file(s) for analysing (--input_pe) | |
| 296 | |
| 297 **Job Type** | |
| 298 - MLST only: Reports Sequence Types | |
| 299 - MLST and VFDB: Reports Sequence Types and user can choose one of the built-in Virulence Factor Datebase (VFDB) strains | |
| 300 - MLST and custom database: Reports Sequence Types and user can upload their own custom database | |
| 301 - VFDB only: Use can choose one of the built-in Virulence Factor Databasse (VFDB) strains | |
| 302 - Custom database only: Use can upload their own custom database | |
| 303 | |
| 304 **ST definitions for MLST scheme:** | |
| 305 - Required if you want to calculate STs (--mlst_definitions) | |
| 306 | |
| 307 **Fasta file of MLST alleles:** | |
| 308 - Required if you want to calculate STs (--mlst_db) | |
| 309 | |
| 310 **Fasta file for gene database:** | |
| 311 - Required if you want details of the sequences. The user must provide their own database (--gene_db) | |
| 312 | |
| 313 **VFDB strain:** | |
| 314 - Required if you want details of the sequences. The use may choose one of the listed strains (--gene_db) | |
| 315 | |
| 316 **Read file type:** | |
| 317 - fastq | |
| 318 - solexa | |
| 319 - fasta | |
| 320 | |
| 321 **Character(s) separating gene name from allele number in MLST database:** | |
| 322 - Required for all MLST job types | |
| 323 - Typically either _ or - | |
| 324 - The output from getMLST will identify the delimiter. | |
| 325 | |
| 326 **Maximum number of mismatches per read for MLST allele calling:** | |
| 327 - Required for all MLST job types | |
| 328 - For MLST schemas with inserts this number should be set to a high value (recommended: 250) | |
| 329 | |
| 330 **Maximum number of mismatches per read for gene allele calling:** | |
| 331 - Required for all VDFB or custom database job types | |
| 332 - For genes with inserts this number should be set to a high value (recommended: 250). | |
| 333 | |
| 334 **Option Type:** | |
| 335 - Basic: Includes only the options listed above | |
| 336 - Advanced: Includes the options listed below | |
| 337 | |
| 338 ------------------------------- | |
| 339 | |
| 340 Advanced Options | |
| 341 ---------------- | |
| 342 | |
| 343 **Minimum %coverage cutoff for gene reporting:** | |
| 344 - Default is 90 (--min_coverage) | |
| 345 | |
| 346 **Maximum %divergence cutoff for gene reporting:** | |
| 347 - Default is 10 (--max_divergence) | |
| 348 | |
| 349 **Minimum mean depth to flag as dubious allele call:** | |
| 350 - Default is 5 (--min_depth) | |
| 351 | |
| 352 **Minimum edge depth to flag as dubious allele call:** | |
| 353 - Default is 2 (--min_edge_depth) | |
| 354 | |
| 355 **Probability of sequencing error:** | |
| 356 - Default is 0.01 (--prob_err) | |
| 357 | |
| 358 **Stop mapping after this number of reads have been mapped (otherwise map all):** | |
| 359 - Default maps all (--stop_after) | |
| 360 | |
| 361 **Other arguments to pass to bowtie2:** | |
| 362 --other | |
| 363 | |
| 364 **Samtools -q parameter:** | |
| 365 - Default is 1 (--mapq) | |
| 366 | |
| 367 **Samtools -Q parameter:** | |
| 368 - Default is 20 (--baseq) | |
| 369 | |
| 370 **Bowtie2 -I/--minins:** | |
| 371 - The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. | |
| 372 - The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. | |
| 373 - Default: 0 (essentially imposing no minimum) | |
| 374 | |
| 375 **Bowtie2 -X/--maxins:** | |
| 376 - The maximum fragment length for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. | |
| 377 - The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. | |
| 378 - Default: 500. | |
| 379 | |
| 380 **Acknowledgments** | |
| 381 Original Author: Mariam Iskander | |
| 382 | |
| 383 Jen Cabral | |
| 384 | |
| 385 Philip Mabon | |
| 386 | |
| 387 Mark Iskander | |
| 388 | |
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389 Eric Enns |
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390 |
| 0 | 391 </help> |
| 392 <citations> | |
| 393 <citation type="doi">10.1128/AAC.01310-13</citation> | |
| 394 </citations> | |
| 395 </tool> |