| Previous changeset 6:3c09557ac425 (2019-04-30) Next changeset 8:da787fc8b740 (2019-06-24) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23 |
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modified:
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 |
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| diff -r 3c09557ac425 -r f1adc47e017a staramr_search.xml --- a/staramr_search.xml Tue Apr 30 15:50:46 2019 -0400 +++ b/staramr_search.xml Thu May 16 15:29:53 2019 -0400 |
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| b'@@ -1,7 +1,7 @@\n <tool id="staramr_search" name="staramr" version="@VERSION@">\n <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>\n <macros>\n-\t <token name="@VERSION@">0.5.0</token>\n+\t <token name="@VERSION@">0.5.1</token>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">staramr</requirement>\n@@ -212,7 +212,7 @@\n A summary of all detected AMR genes/mutations in each genome, one genome per line.\n \n +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+\n-| Isolate ID | Genotype | Predicted Phenotype | Plasmid Genes |\n+| Isolate ID | Genotype | Predicted Phenotype | Plasmid |\n +============+===========================================================+===========================================================================================================+=====================================+\n | 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 |\n +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+\n@@ -222,47 +222,47 @@\n detailed_summary.tsv\n ````````````````````\n \n-A detailed summary of all detected AMR genes/mutations/plasmids in each genome, one gene per line.\n+A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.\n \n-+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n-| Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type |\n-+============+=============+===================================+===========+==========+=========================+=============+========+========+===========+============+\n-| SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid |\n-+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n-| SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid |\n-+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n-| SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid |\n-+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n-| SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid |\n-+------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------'..b'-+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n+| SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid |\n++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n+| SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid |\n++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n+| SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid |\n++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n+| SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid |\n++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n+| SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance |\n++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n+| SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance |\n++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n+| SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance |\n++------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+\n \n \n resfinder.tsv\n@@ -293,10 +293,10 @@\n plasmidfinder.tsv\n `````````````````\n \n-A tabular file of each AMR plasmid gene and additional BLAST information from the **PlasmidFinder** database, one plasmid gene per line.\n+A tabular file of each AMR plasmid type and additional BLAST information from the **PlasmidFinder** database, one plasmid type per line.\n \n +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+\n-| Isolate ID | Gene | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |\n+| Isolate ID | Plasmid | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |\n +============+===========+===========+==========+=========================+=============+=======+=======+===========+\n | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |\n +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+\n@@ -336,7 +336,7 @@\n ::\n \n command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta\n- version = 0.5.0\n+ version = 0.5.1\n start_time = 2019-04-25 16:01:32\n end_time = 2019-04-25 16:01:34\n total_minutes = 0.04\n' |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test1-detailed-summary.tsv --- 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 |
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| @@ -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 |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test1-plasmidfinder.tsv --- 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 |
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| @@ -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 |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test1-summary.tsv --- 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 |
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| @@ -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 |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test2-summary.tsv --- 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 |
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| @@ -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 |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test3-summary.tsv --- 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 |
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| @@ -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 |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test4-summary.tsv --- 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 |
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| @@ -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 |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test5-summary.tsv --- 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 |
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| @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Genes +Isolate ID Genotype Predicted Phenotype Plasmid test-aminoglycoside.fsa None Sensitive None |
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| diff -r 3c09557ac425 -r f1adc47e017a test-data/test6-summary.tsv --- 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 |
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| @@ -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 |