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Commit message:
planemo upload for repository https://github.com/phac-nml/biohansel commit 759c65786566b73806fccaed05802fe01ec4226a |
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modified:
biohansel.xml test-data/SRR1002850_SMALL.fasta-match_results.tab test-data/SRR1002850_SMALL.fasta-results.tab test-data/SRR5646583_SMALL-match_results.tab test-data/SRR5646583_SMALL-results.tab test-data/SRR5646583_SMALL-tech_results.tab |
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| diff -r 3360158bb0c5 -r 4fa9d5e748d4 biohansel.xml --- a/biohansel.xml Mon May 13 09:42:08 2019 -0400 +++ b/biohansel.xml Tue May 21 15:05:40 2019 -0400 |
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| b'@@ -1,7 +1,7 @@\n-<tool id="biohansel" name="biohansel" version="2.1.6">\n+<tool id="biohansel" name="biohansel" version="2.2.0">\n <description>SNP subtyping of genome sequence reads or assemblies</description>\n <requirements>\n- <requirement type="package" version="2.1.1">bio_hansel</requirement>\n+ <requirement type="package" version="2.2.0">bio_hansel</requirement>\n </requirements>\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -129,14 +129,14 @@\n #if $qc_vals.low_cov_depth_freq\n --low-cov-depth-freq $qc_vals.low_cov_depth_freq\n #end if\n-#if $qc_vals.max_missing_tiles\n- --max-missing-tiles $qc_vals.max_missing_tiles\n+#if $qc_vals.max_missing_kmers\n+ --max-missing-kmers $qc_vals.max_missing_kmers\n #end if\n-#if $qc_vals.min_ambiguous_tiles\n- --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles\n+#if $qc_vals.min_ambiguous_kmers\n+ --min-ambiguous-kmers $qc_vals.min_ambiguous_kmers\n #end if\n-#if $qc_vals.max_intermediate_tiles\n- --max-intermediate-tiles $qc_vals.max_intermediate_tiles\n+#if $qc_vals.max_intermediate_kmers\n+ --max-intermediate-kmers $qc_vals.max_intermediate_kmers\n #end if\n #if $qc_vals.low_coverage_warning\n --low-cov-warning $qc_vals.low_coverage_warning\n@@ -200,6 +200,9 @@\n label="Included SNP Subtyping Scheme">\n <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>\n <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>\n+ <option value="typhi">Salmonella Typhi subtyping scheme</option>\n+ <option value="typhimurium">Salmonella Typhimurium subtyping scheme</option>\n+ <option value="tb_speciation">Mycobacterium Tuberculosis subtyping scheme</option>\n </param>\n </when>\n <when value="custom">\n@@ -237,28 +240,28 @@\n optional="true"\n label="QC: Frequency below this coverage are considered low coverage"\n help="default = 20"/>\n- <param name="min_ambiguous_tiles" type="integer"\n- argument="--min-ambiguous-tiles"\n+ <param name="min_ambiguous_kmers" type="integer"\n+ argument="--min-ambiguous-kmers"\n optional="true"\n value="3" min="0"\n- label="QC: Min number of tiles missing for Ambiguous Result"\n+ label="QC: Min number of kmers missing for Ambiguous Result"\n help="default = 3"/>\n- <param name="max_missing_tiles" type="float"\n- argument="--max-missing-tiles"\n+ <param name="max_missing_kmers" type="float"\n+ argument="--max-missing-kmers"\n optional="true"\n value="0.05" min="0" max="1"\n- label="QC: Decimal Proportion of max allowed missing tiles" help="default = 0.05, valid values {0.0 - 1.0}"/>\n- <param name="max_intermediate_tiles" type="float"\n- argument="--max-intermediate-tiles"\n+ label="QC: Decimal Proportion of max allowed missing kmers" help="default = 0.05, valid values {0.0 - 1.0}"/>\n+ <param name="max_intermediate_kmers" type="float"\n+ argument="--max-intermediate-kmers"\n optional="true"\n value="0.05" min="0" max="1"\n- label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype"\n+ label="QC: Decimal Proportion of max allowed missing kmers for an intermediate subtype"\n help="default = 0.05, valid values {0.0 - 1.0}"/> \n <param name="low_coverage_warning" type="integer"\n argument="--low-cov-warning"\n optional="true"\n value="20"\n- label="QC: Overall tile coverage below this value will trigger a low coverage warning"\n+ label="QC: Overall kmer coverage below this value will trigger a low coverage warning"\n help="default = 20"/> \n </section>\n <section name="dev_args" title="Developer Options" expanded="False">\n@@ -342,11 +345,11 @@\n **Usage**\n \n 1) Select the sequence data you wish to subtype (FASTAs or FASTQs)\n-2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg subtyping sch'..b'-----+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+\n | 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 | |\n +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+\n@@ -388,7 +391,7 @@\n Contents of ``match_results.tab``:\n \n +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+\n- | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |\n+ | kmername | seq | freq | refposition | subtype | is_pos_kmer | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |\n +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+\n | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |\n +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+\n@@ -424,8 +427,8 @@\n <citations>\n <citation type="bibtex">@ARTICLE{a1,\n title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},\n- author = {Genevi\xc3\xa8ve Labb\xc3\xa9, 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},\n- url = {https://github.com/phac-nml/bio_hansel}\n+ author = {Genevi\xc3\xa8ve Labb\xc3\xa9, 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},\n+ url = {https://github.com/phac-nml/biohansel}\n }\n }</citation>\n </citations>\n' |
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| diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR1002850_SMALL.fasta-match_results.tab --- a/test-data/SRR1002850_SMALL.fasta-match_results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR1002850_SMALL.fasta-match_results.tab Tue May 21 15:05:40 2019 -0400 |
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| @@ -1,4 +1,4 @@ -tilename seq is_revcomp contig_id match_index refposition subtype is_pos_tile sample file_path scheme scheme_version qc_status qc_message +kmername seq is_revcomp contig_id match_index refposition subtype is_pos_kmer sample file_path scheme scheme_version qc_status qc_message 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 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 2069216-2.2.2 ATACTTAGGCTGTCAGTAACCCGTGAGGTAGTG True NODE_1_length_726282_cov_40.4705_ID_1 99475 2069216 2.2.2 True SRR1002850_SMALL SRR1002850_SMALL.fasta heidelberg 0.5.0 PASS |
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| diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR1002850_SMALL.fasta-results.tab --- a/test-data/SRR1002850_SMALL.fasta-results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR1002850_SMALL.fasta-results.tab Tue May 21 15:05:40 2019 -0400 |
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| @@ -1,2 +1,2 @@ -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 +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 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 |
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| diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR5646583_SMALL-match_results.tab --- a/test-data/SRR5646583_SMALL-match_results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR5646583_SMALL-match_results.tab Tue May 21 15:05:40 2019 -0400 |
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| @@ -1,4 +1,4 @@ -tilename seq freq refposition subtype is_pos_tile is_kmer_freq_okay sample scheme scheme_version qc_status qc_message +kmername seq freq refposition subtype is_pos_kmer is_kmer_freq_okay sample scheme scheme_version qc_status qc_message negative4642573-1.2 TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT 62 4642573 1.2 False True SRR5646583_SMALL heidelberg 0.5.0 PASS 21097-2.2.1.1.1 GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT 42 21097 2.2.1.1.1 True True SRR5646583_SMALL heidelberg 0.5.0 PASS negative3647258-2.2.2.2.2.1 TACGGGTAACTGTTATCGGTAACATTGTCCAAC 64 3647258 2.2.2.2.2.1 False True SRR5646583_SMALL heidelberg 0.5.0 PASS |
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| diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR5646583_SMALL-results.tab --- a/test-data/SRR5646583_SMALL-results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR5646583_SMALL-results.tab Tue May 21 15:05:40 2019 -0400 |
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| @@ -1,2 +1,2 @@ -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 +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 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 |
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| diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR5646583_SMALL-tech_results.tab --- a/test-data/SRR5646583_SMALL-tech_results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR5646583_SMALL-tech_results.tab Tue May 21 15:05:40 2019 -0400 |
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| @@ -1,2 +1,2 @@ -sample subtype avg_tile_coverage qc_status qc_message +sample subtype avg_kmer_coverage qc_status qc_message SRR5646583_SMALL 2.2.1.1.1.1 42.631 PASS |