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planemo upload for repository https://github.com/phac-nml/biohansel commit 759c65786566b73806fccaed05802fe01ec4226a
author nml
date Tue, 21 May 2019 15:05:40 -0400
parents 3360158bb0c5
children e305df0b1af7
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7:3360158bb0c5 8:4fa9d5e748d4
1 <tool id="biohansel" name="biohansel" version="2.1.6"> 1 <tool id="biohansel" name="biohansel" version="2.2.0">
2 <description>SNP subtyping of genome sequence reads or assemblies</description> 2 <description>SNP subtyping of genome sequence reads or assemblies</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.1">bio_hansel</requirement> 4 <requirement type="package" version="2.2.0">bio_hansel</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 <![CDATA[ 7 <![CDATA[
8 8
9 #import re 9 #import re
127 --max-kmer-freq $kmer_vals.kmer_max 127 --max-kmer-freq $kmer_vals.kmer_max
128 #end if 128 #end if
129 #if $qc_vals.low_cov_depth_freq 129 #if $qc_vals.low_cov_depth_freq
130 --low-cov-depth-freq $qc_vals.low_cov_depth_freq 130 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
131 #end if 131 #end if
132 #if $qc_vals.max_missing_tiles 132 #if $qc_vals.max_missing_kmers
133 --max-missing-tiles $qc_vals.max_missing_tiles 133 --max-missing-kmers $qc_vals.max_missing_kmers
134 #end if 134 #end if
135 #if $qc_vals.min_ambiguous_tiles 135 #if $qc_vals.min_ambiguous_kmers
136 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles 136 --min-ambiguous-kmers $qc_vals.min_ambiguous_kmers
137 #end if 137 #end if
138 #if $qc_vals.max_intermediate_tiles 138 #if $qc_vals.max_intermediate_kmers
139 --max-intermediate-tiles $qc_vals.max_intermediate_tiles 139 --max-intermediate-kmers $qc_vals.max_intermediate_kmers
140 #end if 140 #end if
141 #if $qc_vals.low_coverage_warning 141 #if $qc_vals.low_coverage_warning
142 --low-cov-warning $qc_vals.low_coverage_warning 142 --low-cov-warning $qc_vals.low_coverage_warning
143 #end if 143 #end if
144 ]]> 144 ]]>
198 <when value="standard"> 198 <when value="standard">
199 <param name="scheme_type" type="select" 199 <param name="scheme_type" type="select"
200 label="Included SNP Subtyping Scheme"> 200 label="Included SNP Subtyping Scheme">
201 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option> 201 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
202 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option> 202 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
203 <option value="typhi">Salmonella Typhi subtyping scheme</option>
204 <option value="typhimurium">Salmonella Typhimurium subtyping scheme</option>
205 <option value="tb_speciation">Mycobacterium Tuberculosis subtyping scheme</option>
203 </param> 206 </param>
204 </when> 207 </when>
205 <when value="custom"> 208 <when value="custom">
206 <param name="scheme_input" 209 <param name="scheme_input"
207 type="data" format="fasta" 210 type="data" format="fasta"
235 argument="--low-cov-depth-freq" 238 argument="--low-cov-depth-freq"
236 value="20" min="0" 239 value="20" min="0"
237 optional="true" 240 optional="true"
238 label="QC: Frequency below this coverage are considered low coverage" 241 label="QC: Frequency below this coverage are considered low coverage"
239 help="default = 20"/> 242 help="default = 20"/>
240 <param name="min_ambiguous_tiles" type="integer" 243 <param name="min_ambiguous_kmers" type="integer"
241 argument="--min-ambiguous-tiles" 244 argument="--min-ambiguous-kmers"
242 optional="true" 245 optional="true"
243 value="3" min="0" 246 value="3" min="0"
244 label="QC: Min number of tiles missing for Ambiguous Result" 247 label="QC: Min number of kmers missing for Ambiguous Result"
245 help="default = 3"/> 248 help="default = 3"/>
246 <param name="max_missing_tiles" type="float" 249 <param name="max_missing_kmers" type="float"
247 argument="--max-missing-tiles" 250 argument="--max-missing-kmers"
248 optional="true" 251 optional="true"
249 value="0.05" min="0" max="1" 252 value="0.05" min="0" max="1"
250 label="QC: Decimal Proportion of max allowed missing tiles" help="default = 0.05, valid values {0.0 - 1.0}"/> 253 label="QC: Decimal Proportion of max allowed missing kmers" help="default = 0.05, valid values {0.0 - 1.0}"/>
251 <param name="max_intermediate_tiles" type="float" 254 <param name="max_intermediate_kmers" type="float"
252 argument="--max-intermediate-tiles" 255 argument="--max-intermediate-kmers"
253 optional="true" 256 optional="true"
254 value="0.05" min="0" max="1" 257 value="0.05" min="0" max="1"
255 label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" 258 label="QC: Decimal Proportion of max allowed missing kmers for an intermediate subtype"
256 help="default = 0.05, valid values {0.0 - 1.0}"/> 259 help="default = 0.05, valid values {0.0 - 1.0}"/>
257 <param name="low_coverage_warning" type="integer" 260 <param name="low_coverage_warning" type="integer"
258 argument="--low-cov-warning" 261 argument="--low-cov-warning"
259 optional="true" 262 optional="true"
260 value="20" 263 value="20"
261 label="QC: Overall tile coverage below this value will trigger a low coverage warning" 264 label="QC: Overall kmer coverage below this value will trigger a low coverage warning"
262 help="default = 20"/> 265 help="default = 20"/>
263 </section> 266 </section>
264 <section name="dev_args" title="Developer Options" expanded="False"> 267 <section name="dev_args" title="Developer Options" expanded="False">
265 <param name="use_json" 268 <param name="use_json"
266 type="boolean" 269 type="boolean"
340 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes. 343 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes.
341 344
342 **Usage** 345 **Usage**
343 346
344 1) Select the sequence data you wish to subtype (FASTAs or FASTQs) 347 1) Select the sequence data you wish to subtype (FASTAs or FASTQs)
345 2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg subtyping scheme, *Salmonella enterica* serovar Enteritidis subtyping scheme, or your own custom `biohansel` compatible subtyping scheme) 348 2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg, Enteritidis, Typhimurium, or Typhi subtyping scheme, or your own custom `biohansel` compatible subtyping scheme)
346 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results 349 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results
347 4) Click ``Execute`` 350 4) Click ``Execute``
348 351
349 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_. 352 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_ or the `biohansel read the docs page <https://bio-hansel.readthedocs.io/en/readthedocs/>`_.
350 353
351 354
352 **Example analysis results of a single FASTA file** 355 **Example analysis results of a single FASTA file**
353 356
354 Contents of ``results.tab``: 357 Contents of ``results.tab``:
355 358
356 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ 359 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
357 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | qc_status | qc_message | 360 | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | qc_status | qc_message |
358 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ 361 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
359 | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | | 362 | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | |
360 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ 363 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
361 364
362 365
363 Contents of ``match_results.tab``: 366 Contents of ``match_results.tab``:
364 367
365 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ 368 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
366 | tilename | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_tile | sample | file_path | scheme | scheme_version | qc_status | qc_message | 369 | kmername | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_kmer | sample | file_path | scheme | scheme_version | qc_status | qc_message |
367 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ 370 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
368 | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | | 371 | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
369 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ 372 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
370 | negative2131791-2.2.3.1.3 | GCTGGGCGAAATGATGCAGTTCACCACTTGCTC | True | NODE_1_length_726282_cov_40.4705_ID_1 | 36900 | 2131791 | 2.2.3.1.3 | False | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | | 373 | negative2131791-2.2.3.1.3 | GCTGGGCGAAATGATGCAGTTCACCACTTGCTC | True | NODE_1_length_726282_cov_40.4705_ID_1 | 36900 | 2131791 | 2.2.3.1.3 | False | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
371 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ 374 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
378 381
379 382
380 Contents of ``results.tab``: 383 Contents of ``results.tab``:
381 384
382 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ 385 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
383 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | avg_tile_coverage | qc_status | qc_message | 386 | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | avg_kmer_coverage | qc_status | qc_message |
384 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ 387 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
385 | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | | 388 | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | |
386 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ 389 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
387 390
388 Contents of ``match_results.tab``: 391 Contents of ``match_results.tab``:
389 392
390 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ 393 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
391 | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message | 394 | kmername | seq | freq | refposition | subtype | is_pos_kmer | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |
392 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ 395 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
393 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | | 396 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
394 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ 397 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
395 | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | | 398 | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
396 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ 399 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
422 425
423 ]]></help> 426 ]]></help>
424 <citations> 427 <citations>
425 <citation type="bibtex">@ARTICLE{a1, 428 <citation type="bibtex">@ARTICLE{a1,
426 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America}, 429 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},
427 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash}, 430 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, David Son, Darian Hole, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash},
428 url = {https://github.com/phac-nml/bio_hansel} 431 url = {https://github.com/phac-nml/biohansel}
429 } 432 }
430 }</citation> 433 }</citation>
431 </citations> 434 </citations>
432 </tool> 435 </tool>