Mercurial > repos > nml > staramr
changeset 7:f1adc47e017a draft
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
| author | nml |
|---|---|
| date | Thu, 16 May 2019 15:29:53 -0400 |
| parents | 3c09557ac425 |
| children | da787fc8b740 |
| files | staramr_search.xml test-data/test1-detailed-summary.tsv test-data/test1-plasmidfinder.tsv test-data/test1-summary.tsv test-data/test2-summary.tsv test-data/test3-summary.tsv test-data/test4-summary.tsv test-data/test5-summary.tsv test-data/test6-summary.tsv |
| diffstat | 9 files changed, 53 insertions(+), 53 deletions(-) [+] |
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--- a/staramr_search.xml Tue Apr 30 15:50:46 2019 -0400 +++ b/staramr_search.xml Thu May 16 15:29:53 2019 -0400 @@ -1,7 +1,7 @@ <tool id="staramr_search" name="staramr" version="@VERSION@"> <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> <macros> - <token name="@VERSION@">0.5.0</token> + <token name="@VERSION@">0.5.1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> @@ -212,7 +212,7 @@ A summary of all detected AMR genes/mutations in each genome, one genome per line. +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ -| Isolate ID | Genotype | Predicted Phenotype | Plasmid Genes | +| Isolate ID | Genotype | Predicted Phenotype | Plasmid | +============+===========================================================+===========================================================================================================+=====================================+ | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ @@ -222,47 +222,47 @@ detailed_summary.tsv ```````````````````` -A detailed summary of all detected AMR genes/mutations/plasmids in each genome, one gene per line. +A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line. -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type | -+============+=============+===================================+===========+==========+=========================+=============+========+========+===========+============+ -| SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ -| SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance | -+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| Isolate ID | Gene/Plasmid | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type | ++============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+ +| SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance | ++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ resfinder.tsv @@ -293,10 +293,10 @@ plasmidfinder.tsv ````````````````` -A tabular file of each AMR plasmid gene and additional BLAST information from the **PlasmidFinder** database, one plasmid gene per line. +A tabular file of each AMR plasmid type and additional BLAST information from the **PlasmidFinder** database, one plasmid type per line. +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ -| Isolate ID | Gene | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | +| Isolate ID | Plasmid | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | +============+===========+===========+==========+=========================+=============+=======+=======+===========+ | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ @@ -336,7 +336,7 @@ :: command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta - version = 0.5.0 + version = 0.5.1 start_time = 2019-04-25 16:01:32 end_time = 2019-04-25 16:01:34 total_minutes = 0.04
--- a/test-data/test1-detailed-summary.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test1-detailed-summary.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,4 +1,4 @@ -Isolate ID Gene Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession Data Type +Isolate ID Gene/Plasmid Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession Data Type 16S-rc_gyrA-rc_beta-lactam.fsa None Plasmid 16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) spectinomycin 99.94 100.0 1544/1544 16S_rrsD 1604 61 Resistance 16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456 Resistance
--- a/test-data/test1-plasmidfinder.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test1-plasmidfinder.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,1 +1,1 @@ -Isolate ID Gene %Identity %Overlap HSP Length/Total Length Contig Start End Accession +Isolate ID Plasmid %Identity %Overlap HSP Length/Total Length Contig Start End Accession
--- a/test-data/test1-summary.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test1-summary.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Genes +Isolate ID Genotype Predicted Phenotype Plasmid 16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T), blaIMP-42, gyrA (A67P) spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid None
--- a/test-data/test2-summary.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test2-summary.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Genes +Isolate ID Genotype Predicted Phenotype Plasmid 16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None
--- a/test-data/test3-summary.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test3-summary.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Genes +Isolate ID Genotype Predicted Phenotype Plasmid 16S-rc_gyrA-rc_beta-lactam.fsa None Sensitive None
--- a/test-data/test4-summary.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test4-summary.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Genes +Isolate ID Genotype Predicted Phenotype Plasmid 16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa None Sensitive None
--- a/test-data/test5-summary.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test5-summary.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Genes +Isolate ID Genotype Predicted Phenotype Plasmid test-aminoglycoside.fsa None Sensitive None
--- a/test-data/test6-summary.tsv Tue Apr 30 15:50:46 2019 -0400 +++ b/test-data/test6-summary.tsv Thu May 16 15:29:53 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Genes +Isolate ID Genotype Predicted Phenotype Plasmid test-aminoglycoside.fsa aac(6')-Iaa gentamicin None