Mercurial > repos > iuc > sonneityping
changeset 0:db4fe7172114 draft
"planemo upload for repository https://github.com/katholt/sonneityping commit 1b4231e8f98a234c29f57fef400f58f14645dc95"
| author | iuc |
|---|---|
| date | Thu, 16 Sep 2021 06:52:18 +0000 |
| parents | |
| children | 0ac12c344bfa |
| files | macros.xml parse_mykrobe_predict.xml test-data/SRR6114360.json test-data/alleles.txt |
| diffstat | 4 files changed, 451 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Sep 16 06:52:18 2021 +0000 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">sonneityping</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">20210201</token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parse_mykrobe_predict.xml Thu Sep 16 06:52:18 2021 +0000 @@ -0,0 +1,71 @@ +<tool id="sonneityping" name="parse mykrobe predict" version="@TOOL_VERSION@" profile="20.05"> + <description>for Shigella sonnei and tabulate results into a single tab-delimited file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + parse_mykrobe_predict --jsons + + #for $i in $json + '$i' + #end for + + #if $optional.alleles: + --alleles '$optional.alleles' + #end if + + --prefix results + + ]]></command> + <inputs> + <param name="json" type="data" format="json" multiple="true" optional="false" label="Mykrobe results to parse." help="Mykrobe predict results in JSON format." /> + + <section name="optional" title="Optional Parameters" expanded="false"> + <param name="alleles" type="data" format="txt,tabular" optional="true" label="Alleles" help="Links each lineage name to its human-readable counterpart." /> + </section> + </inputs> + <outputs> + <data format="tabular" label="parsed output" name="parsed_output" from_work_dir="results_predictResults.tsv" /> + </outputs> + <tests> + <test> + <param name="json" ftype="json" value="SRR6114360.json"/> + <param name="optional.alleles" ftype="txt" value="alleles.txt" /> + <output name="parsed_output"> + <assert_contents> + <has_text text="3.7.30.4" /> + <has_text text="S. sonnei" /> + </assert_contents> + </output> + </test> + <test> + <param name="json" ftype="json" value="SRR6114360.json"/> + <output name="parsed_output"> + <assert_contents> + <has_text text="3.7.30.4" /> + <has_text text="S. sonnei" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Parse Mykrobe Predict +===================== + +Parses Mykrobe predict results for Shigella sonnei. + +Mykrobe v0.9.0+ can identify input genomes as S. sonnei, assign those identified as S. sonnei to hierarchical genotypes based on detection of single nucleotide variants (SNVs; defined in the file alleles.txt), and report known mutations in the quinolone-resistance determining region (QRDR) of genes gyrA (S83L, D87G, D87Y) and parC (S80I). + +Details of the genotyping scheme are available in the paper Hawkey et al, 2021, Nature Communications. Proposals for new genotype definitions to be added to the scheme can be submitted as an Issue in this repository.]]></help> + <citations> + <citation type="bibtex"> + @misc{GitHubsonneityping, + title = {sonneityping}, + journal = {GitHub Repository}, + url = {https://github.com/katholt/sonneityping}, + } + </citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR6114360.json Thu Sep 16 06:52:18 2021 +0000 @@ -0,0 +1,223 @@ +{ + "SRR6114360": { + "susceptibility": { + "quinolones": { + "predict": "S" + } + }, + "phylogenetics": { + "phylo_group": { + "Ecoli_Shigella": { + "percent_coverage": 100.0, + "median_depth": 26 + } + }, + "sub_complex": { + "Unknown": { + "percent_coverage": -1, + "median_depth": -1 + } + }, + "species": { + "Shigella_sonnei": { + "percent_coverage": 95.163, + "median_depth": 22.0 + } + }, + "lineage": { + "lineage": [ + "lineage3.7.30.4" + ], + "calls_summary": { + "lineage3.7.30.4": { + "good_nodes": 4, + "tree_depth": 4, + "genotypes": { + "lineage3": 1, + "lineage3.7": 1, + "lineage3.7.30": 1, + "lineage3.7.30.4": 1 + } + } + }, + "calls": { + "lineage3.7.30.4": { + "lineage3": { + "C59602T": { + "variant": "ref-C59602T?var_name=C59602T&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=C59602T", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -3282.0148702940733, + -99999999, + -19.32539954665346 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 0.0, + "median_depth": 0, + "min_non_zero_depth": 0, + "kmer_count": 0, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 27, + "min_non_zero_depth": 26, + "kmer_count": 541, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [], + "conf": 3263 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage3.7": { + "G4080478A": { + "variant": "ref-G4080478A?var_name=G4080478A&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=G4080478A", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -3961.55750528479, + -99999999, + -39.85243726626552 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 0.0, + "median_depth": 0, + "min_non_zero_depth": 0, + "kmer_count": 0, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 34, + "min_non_zero_depth": 34, + "kmer_count": 702, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [], + "conf": 3922 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage3.7.30": { + "A1138004G": { + "variant": "ref-A1138004G?var_name=A1138004G&num_alts=2&ref=NC_016822&enum=0&gene=NA&mut=A1138004G", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -1607.6280372631725, + -99999999, + -477.52941234336663 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 0.0, + "median_depth": 0, + "min_non_zero_depth": 0, + "kmer_count": 0, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 1, + "min_non_zero_depth": 1, + "kmer_count": 20, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [ + "LOW_TOTAL_DEPTH" + ], + "conf": 1130 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage3.7.30.4": { + "G3082193A": { + "variant": "ref-G3082193A?var_name=G3082193A&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=G3082193A", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -2726.2314885023525, + -99999999, + -40.69232343956539 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 0.0, + "median_depth": 0, + "min_non_zero_depth": 0, + "kmer_count": 0, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 20, + "min_non_zero_depth": 18, + "kmer_count": 400, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [], + "conf": 2686 + }, + "_cls": "Call.VariantCall" + } + } + } + } + } + }, + "kmer": 21, + "probe_sets": [ + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.lineage.20210201.probes.fa.gz", + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.mlst.20201010.sonnei.fa.gz", + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.probe.uidA.20201010.fa.gz", + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.qrdr.20201010.probes.fa.gz" + ], + "files": [ + "SRR6114360_1" + ], + "version": { + "mykrobe-predictor": "v0.10.0", + "mykrobe-atlas": "v0.10.0" + }, + "genotype_model": "kmer_count" + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alleles.txt Thu Sep 16 06:52:18 2021 +0000 @@ -0,0 +1,148 @@ +159897 C 1 Lineage I lineage1 +204118 G 1.1 - lineage1.1 +1173345 T 1.2 - lineage1.2 +494060 C 1.3 - lineage1.3 +434389 T 1.4 - lineage1.4 +3465611 A 1.5 - lineage1.5 +2164632 C 1.5.1 - lineage1.5.1 +2138308 A 1.5.2 - lineage1.5.2 +220353 T 1.5.3 - lineage1.5.3 +1411472 A 1.6 - lineage1.6 +59422 C 1.6.1 - lineage1.6.1 +452958 G 1.6.2 - lineage1.6.2 +4108759 A 1.6.3 - lineage1.6.3 +4180475 A 1.6.4 - lineage1.6.4 +4967081 G 2 Lineage II lineage2 +3922942 A 2.1 - lineage2.1 +81464 T 2.1.1 - lineage2.1.1 +765305 T 2.1.2 - lineage2.1.2 +1148833 T 2.1.3 - lineage2.1.3 +2751379 A 2.1.4 - lineage2.1.4 +3209745 G 2.1.5 - lineage2.1.5 +2163231 A 2.1.6 - lineage2.1.6 +4969251 T 2.1.7 - lineage2.1.7 +3277620 A 2.1.8 - lineage2.1.8 +2964241 C 2.2 - lineage2.2 +3231002 A 2.3 - lineage2.3 +3209436 A 2.4 - lineage2.4 +4418301 A 2.4.1 - lineage2.4.1 +1995501 A 2.4.2 - lineage2.4.2 +2693836 A 2.4.3 - 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