| Next changeset 1:8e8dc9a1e3e5 (2017-10-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty |
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added:
mlst.xml mlst_list.xml test-data/Acetobacter.fna test-data/MRSA0252_trimmed.fna test-data/output_list.txt test-data/output_longlist.txt test-data/output_mincov100.txt test-data/output_minid100.txt test-data/output_mrsa.txt test-data/output_noresults.txt tool_dependencies.xml |
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| diff -r 000000000000 -r 735872ff8222 mlst.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mlst.xml Mon Dec 12 15:07:38 2016 -0500 |
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| @@ -0,0 +1,131 @@ +<tool id="mlst" name="MLST" version="0.1.0"> + <requirements> + <requirement type="package" version="2.6">mlst</requirement> + </requirements> + + <version_command>mlst --version</version_command> + + <command detect_errors="exit_code"><![CDATA[ + mlst "$input_file" --nopath + #if $settings.advanced == "advanced" + #if $settings.min_dna_id + --minid=$settings.min_dna_id + #end if + #if $settings.min_dna_cov + --mincov=$settings.min_dna_cov + #end if + #if $settings.scheme + --scheme=$settings.scheme + #end if + #end if + > "$report" + ]]></command> + + <inputs> + <param type="data" name="input_file" format="fasta,genbank" /> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + <when value="advanced"> + <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" /> + <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" /> + <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" /> + </when> + </conditional> + </inputs> + + <outputs> + <data name="report" format="tabular" /> + </outputs> + + <tests> + <!-- Basic test - will produce no results. --> + <test> + <param name="input_file" value="Acetobacter.fna"/> + <param name="advanced" value="simple"/> + <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/> + </test> + + <!-- Basic test - will produce results. --> + <test> + <param name="input_file" value="MRSA0252_trimmed.fna"/> + <param name="advanced" value="simple"/> + <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/> + </test> + + <!-- Advanced test - Min DNA Coverage 100 --> + <test> + <param name="input_file" value="MRSA0252_trimmed.fna"/> + <param name="advanced" value="advanced"/> + <param name="min_dna_cov" value="100"/> + <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/> + </test> + + <!-- Advanced test - Min DNA ID 100 --> + <test> + <param name="input_file" value="MRSA0252_trimmed.fna"/> + <param name="advanced" value="advanced"/> + <param name="min_dna_id" value="100"/> + <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +Given a genome file in FASTA or Genbank format, MLST will scan the file against PubMLST typing schemes. + +**Output** + +MLST will produce a tab-seperated output file which contains: +- the filename +- the closest PubMLST scheme name +- the ST (sequence type) +- the allele IDs + +**Example Output** + +:: + + genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3) + +**Without auto-detection** + +If you provide the 'scheme' parameter, it will print a fixed tabular output with a heading containing allele names specific to that scheme. To view a list of schemes, use the MLST List tool. + +:: + + FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm + NM003.fa neisseria 11 2 3 4 3 8 4 6 + +**Missing data** +MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below: + ++--------+---------------------------+ +| Symbol | Meaning | ++========+===========================+ +| n | Exact intact allele | ++--------+---------------------------+ +| ~n | Novel allele similar to n | ++--------+---------------------------+ +| n,m | Multiple alleles | ++--------+---------------------------+ +| *-* | Allele missing | ++--------+---------------------------+ + + ]]></help> + + <citations> + <citation type="bibtex"> + @UNPUBLISHED{Seemann2016, + author = "Seemann T", + title = "MLST: Scan contig files against PubMLST typing schemes", + year = "2016", + note = "https://github.com/tseemann/mlst"} + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 735872ff8222 mlst_list.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mlst_list.xml Mon Dec 12 15:07:38 2016 -0500 |
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| @@ -0,0 +1,51 @@ +<tool id="mlst_list" name="MLST List" version="0.1.0"> + <requirements> + <requirement type="package" version="2.6">mlst</requirement> + </requirements> + + <version_command>mlst --version</version_command> + + <command detect_errors="exit_code"><![CDATA[ + mlst $list_type > "$report" + ]]></command> + + <inputs> + <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list" + help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" /> + </inputs> + + <outputs> + <data format="txt" name="report" label="${tool.name} - list of schemes"/> + </outputs> + + <tests> + <!-- Test the longlist option --> + <test> + <param name="list_type" value="true" /> + <output name="report" ftype="txt" file="output_longlist.txt" /> + </test> + + <!-- Test the list option --> + <test> + <param name="list_type" value="false" /> + <output name="report" ftype="txt" file="output_list.txt" /> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +MLST List will list all the scheme names used by MLST. Selecting the long list option will also provide the alleles for all MLST schemes. + + ]]></help> + + <citations> + <citation type="bibtex"> + @UNPUBLISHED{Seemann2016, + author = "Seemann T", + title = "ABRicate: mass screening of contigs for antiobiotic resistance genes", + year = "2016", + note = "https://github.com/tseemann/abricate"} + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 735872ff8222 test-data/Acetobacter.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Acetobacter.fna Mon Dec 12 15:07:38 2016 -0500 |
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| b'@@ -0,0 +1,300 @@\n+>gi|529218539|ref|NC_021976.1| Acetobacter pasteurianus 386B plasmid Apa386Bp1, complete sequence\n+GAAGGAAGCTTGGATCAGCTTCGTGTTTCCCGTGTGCCCCATTTCATTATGCAGTTCCTGAAGAGATCAT\n+CGTGGTTAGGTTGAGTCTCCGATCCGCCATGAGGGAACGTGTAGAATGTAGCGAGTGTCATGAACCATGA\n+CGAACATCGGGAAGAGCGGTAACCGCCAAGGACTGATGAGGTGTGAAGCCAACAGGCTGGTACCATACAG\n+CACATTACGATGTAGACGCTCGTGATCCGGCGATGAGGATATCGACAAGGCGCTTTGCACTAGTTTCCCA\n+ACCGGGGCCAGCCGCATAGTTGGAAACACCAGCCAGAGCACGAAGTAGGTCGAGTGGTTCGATCTCTGTG\n+CTGATATCTCTACTGGCAACTGCGGCTGCTACAAGTTTCTCAATCGCGTTCTGTAGAACCGTGCCAGACT\n+GGGCATAAAGTGCGCTCGTTCCTCCCATCAGCCCATTGAGGGCGGGGGCAATTACCTGCTTGGCAGCAAT\n+ATAATCTACAAACAGTCGCATCCATGCACGCAGTGCCTCCACGGGCGGATGCTGTGTGGCAAGAACTGGT\n+GCCGCGTCGGCTAGGCGGTCCAGTTCAGCGCGATAGACCGCCTCGATCAGAGCATCGCGATTAGGAAAAT\n+GGCGGTAAAGTGTTCCAATTCCAACTGCCGCACGACGGGCAACTTCATCCAAAGGGATATCGATTTCCCC\n+CGCCGTGAACGCGGCTTTGGCCACTTTAAGCAGGTTTTCCCTGTTACGTTGTCCATCGCTGCGCGGTCGG\n+CGGCGCGGCTTTTTTTCGTCGGTCACCGGTTTTCCTCTTGTTAAACGGAGTATGTCTCCGCATATACAAG\n+ACGGAGCCATGCTCCATATAACACTCCGAATGCCGCTTCGGCAAAAAACGGATGATCCTTTCAAGGAGTT\n+CCACCCATGACACAGACTTTTGGCGCGCGTTCGACGACAGAAGATGTCCTTTCCAGCGTGTCCCTAAAGG\n+GCAAACGTGTTCTCGTAACTGGCGTTTCTGCTGGTCTGGGGGTTGAAACCGCGCGTGCCCTTGCGGCTCA\n+TGGTGCCCAGGTAGTGGGGGCCGCGCGTAACCTGACAAAAGCAGAACACGCCACCGGACAGGTCCGTGCA\n+GATGCTGAACGTGGGGGAGGGACGTTTGAACTGATCGCCCTAGACCTCGCGGATCTGACCAGTGTCCGCG\n+CCTGCGCTGACCAATTGAACGCAACCGGTTTGCCTTTCGATCTGGTTATTGCCAATGCGGGTGTGATGGC\n+TACACCATTTAGTCATACGAAGGACGGATTTGAGACGCAGTTCGGCACCAACCACCTAGGGCACTTTGTT\n+CTTGTCAACCAGATAGCGGGGCTGATGCGCCCCGGTGCCCGACTGGTCAATGTCTCCTCGGCCGGACATC\n+GCTTTGCAGATGTTGATCTGAAAGACCCGAATTTCGAGCATACACCATACGATCCATTCATCGCTTATGG\n+ACGTTCTAAAACAGCCAATATCCTTTTTGCCGTTGCGTTTGACGCACGACATCGTACACGTGGTGTGCGT\n+GCTACAGCAGTGCATCCGGGTGGGATCATGACCGAACTGCCGCGCTATATGCAGGCAGGTGCCATTGAGG\n+CAATGGTGGCGGGGATCAATGAACAGGCTGCTGCAGAAGGAAAGCCACCATTTCAGTTTAAGACCATTCC\n+ACAAGGTGCAGCCACATCGGTCTGGGCAGGCGTGGTGGCGGAAGCTGATGCGGTCGGTGGGCATTACAGC\n+GAAGACTGCCATGTAAGCCCGGTTATTCCTGATGATCAGCTTCTTAGCTTGGTCAGTGAAGGTGTGCGGG\n+CCTACGCGGTTGATCCTGTGCATGCCGAGGCGCTGTGGGCAAAAAGTGAGGAAATGGTTGGAGAAACATT\n+TTCCTGAAACATCCACATCCTTGTTTCTGGCATAACGGATAAGCCCGACATCCAGACAGACATTTTGCCG\n+ATATGTGTAGCTTGAGCGCAGGGGACGGAAAACGTTTTTCCTGCGCTTTTCGTGCAAGGATATTGATTGT\n+AGTGCGCCTTGTTGTTTTTGGTTTGCCTCTTCTTGTTGTGATCCTGAATTGGCTGTGGCCATTACCGCTG\n+CCTTTGGGCCTGAAGATGTTTGCAGCCGTTCTGATGATCATGGCCGCACTTTACCACTACTGGTCTCGGC\n+TTTCTTCGGGGTCCGTTTTCACCCCGGAATTCCCCCGGCCTGTTATCATCCTGTTTAATTGGGCGTTCGG\n+GGCCATCCTGTTTCTTACGCTGCTCCAGATTGCGCTGGATTTCGGTGCACTACTGGTTGTGCTGATGACG\n+TGGCAGCCAGTGCATATTCCAGTAGGTGCGCGGGGGGCTGCTGGAGGTATTGCTGGGGTGCTGGCCGCAA\n+TTGGCGTTGCCAATGCGCTACGTGTGCCACCGGTCAGGAACGTGGCAGTGACCATTCCCGGCCTGTCGCC\n+AGCGTTTGACGGGTATCGACTGGTCCAATTGACCGATCTGCATATTAGTCGGCTGTTTCCCGCCAACTGG\n+GCAAGGGCAGTTGTGGACCGTACCAATGCGATCGGTGCTGATATGATTGTCGTGACGGGTGATTTCATTG\n+ACGGCTCAGTAGCCATGCGCCGCGCGGACGTGGCTCCACTTGCACAATTACACGCGCCAGACGGTGTTTT\n+GGCTATCCCGGGCAATCATGAATATTACTTTGATTATACCGACTGGATGCGTCATCTGAAGGAATTGGGC\n+TTTCACATGCTACTGAACCGTCACACAGTCATCTCAAGGGGAGGGGCTGAGTTGGTCATTGCAGGTGTTA\n+CTGATCGGTCCGCACCTAGGCATGGACAGGCTGGCCCCAATCTGGCCGCGGCTCTCACAGATAGTCCCGA\n+AGGGGCCCCGATTGTGCTGCTTGATCACCAACCCGGTGATGCGCGTGCGGCGGCTACCCAAGGTATTGCT\n+CTTCAGTTGTCGGGACATACACATGGCGGGATGATCCTCGGTCTCGACCGTCTTGTTGCGCGCGGGAATA\n+ACGGATTTGTATCCGGGCGCTACGATGTGAATGGCATGACGCTTTACGTCAATAACGGTACCGGGCTGTG\n+GCCAGGCTTTGCGCTTCGGCTGGGCATACCGCCTGAGATCACCTGCTTTAGTTTGCGTGCGGGATAATAC\n+TGGGGTTTTATCAAGTGCTTCTTATAGCACATCTCGCCGCAACCGTGTTCCTTCTCATTTCTTGAGTTAT\n+AGCTTCCTGTAATCACGTGGGCTAACACCTGTTTCCCTGCGAAACACCTGTGCAAAATGGCTTGGGCTCT\n+TATAACCAATGGTCAGGGCGATCTCGATGATGGATTGGTCGCTCTGGCACAAAAGTTCCTTCGCATGTTC\n+AACACGTCGCCGCACAAACCAGCGTGACGGGCTTTGCCCCATGGTGTTGTGAAATGATCGGCTGAAATGA\n+AACCGGCCCATCCCGCACAAATCGGCCAGAACATCCAGATCAAATGGTTCGGCGAGATGTGCCTCCATAT\n+GATCAAGTGCCTTGCGAAGTTTCCAAGCTGGGAGCTGTGCAGGTTTGGGCGTGCGTATCACATGTATATT\n+TGCATAATTGCGCAAAAGGTGGATGGTCAGACTTTCCAAAAGTCCGTTCACAAATAAAGGACTGGCCAAC\n+AGAGGCTTCTGTAGCTCAGCCGTCAGACCTGTCAGAACGCCAGATATAAATGTATCCTGAACACCGGAAA\n+TATCATGCATACGGAGCCGCAATGGGTTAAGCCCCAAAGATCGGGCAGCGCGGTTCACCAAAGTC'..b'TCAGCATGGCCGGTCTGCTGGGGACCGCTCTCATGCTG\n+GCCGAATGTTCAGGCATCGGCATGACCATTATGCTCGATGACATTCCACGGCCTGAGGATGCTCCGATGG\n+AGCGCTGGCTGTCTGCATTCCCAAGCTACGGATACCTGCTGACAGCGCGTCCCGAAGATGCCCACGCGAT\n+CATGGCCCGGTTTCGTGGACGTGGCATTACTGCTTCTGTCATCGGGCGGTGTGAGAGCACGCAGCGGCTG\n+GATGTCATATGGGCGGACGAGAAAGAAACCTTCTGGGATCTCGCCCGGTCCTCACTCATGGGATTTGCGC\n+CATGAGTCTGTCCATTGGCATTCTGACCCATTCGACCAATCCGCGTGGCGGCGTGGTGCACGGCATGGCG\n+CTAGCGGAAACTCTGTGTGACGCGGGCCACGACGCAACGCTGATCGCACCGGACGTGACAGGATCGGGTT\n+TCTTCCGCAAACCCCGTTGCGCGACCTGGTGCATCCCAGCCGCGTCTGTACCTGATCTGCCGACACTGGT\n+GGAGCGTCGTATTGGCGAAATCAGAGACGCATTGCGCGGACAGCATTTTGACGTGCTGCATGCGCAGGAT\n+CCGATCAGCGCCAATGCTTTGGCCGATCTGGTGCAGGAAGGGCGGATACCGGGCTTTGCCCGCACGGTCC\n+ACCATCTTGACCATTTCACGCACCCGGTCCTTGCCGCGCGGCAGGAACGGGGGATCAGGGCGGCGGCCGA\n+ACTGTTTACCGTCAGCACAATGTGGGAAGATGTCCTGCGCAACGGCCATGGCCGCGAAGCTCCGGTCGTG\n+GGCAACGGGGTTGATCCCGTGCGCTTTTCACCCGTAGCAACCGCGCACGATGCCGCGTTGCGAGCGCGGT\n+ATCATCTGCCTGCCGGTCAGCACCTGATCCTGTCCGTGGGCGGGATCGAGCAGCGCAAGAACACGCTGCA\n+CTTGCTCGACGCATTTCTGGCCCTTCGTTGCGAACAGCCTGATGTGCATCTGATTGTGGCAGGCGGGGCC\n+TCGCTGCTGGATCATTCTGCCTACCGCACCCGATTCATGGAGCGTCTGCGCGAAAGCGGTGCGGCCGATC\n+ATGTCACCATCACCGGGCCAGTTGCTGATGAAGACATGCCTTCATTCTACCGGCAGGCGGACGTGTTGGC\n+CTATCCATCCGTAACCGAGGGGTTCGGACTGTGCCCGCTGGAAGCCCTGGCTTGTGGAATCCCCGTGGTG\n+GTGCCAGCCGCGCTACCTTTCACGGAACATTTTTCGGTAACGGATGCGCTGTGGTGCCAACCGGCGCACC\n+CCGACACCTTGTTCATGGCGTTGCGCGACGCCCTGCGCGTCGAAAGCCGTGACCATTTCCGGCTCAGCGG\n+CCCCGCAACAGCCCGCCGTTTCGACTGGGACAGCGTCGCCAGTCGGCATCTCCCCGCATATCGGCGTCTT\n+GCGGCATTACAGCACGCTGACGTCCCGGCTTCAGGAGTTTTGTCACCATGCCCGAAATGACCTTTCGCGT\n+GCGTTGGCCCGATGGGAACGAGACCGACTGTTACTCCCCATCGCTGGTCATAAGGGACCACTTCACACCC\n+GGTCAGGATTATCCGGTCCGGGAGTTTCTTGAAAAGGCGGACACGGCTCTGACCCAGGCGAGCGAACGGG\n+TTCGTGCCCGTTACGGCTTTCCGTGCAGTCGCGCCCTTGGCCAGCTGCACGTCATTCAGCAGAGCAGTGC\n+GCCTTTCCTTAATCGACCCGATGCGCAGGTGCGCGTCCTGTCTTTCAGATACTGAGACGAAAAGAACGAC\n+CATGACACAGAACGAAAAAAGCATTCCTGTTATCATCGTGGGCGGCGGACAGGCTGGCCTCTCCCTGAGC\n+TGGTATCTCTGTCGCGAAAAAGTGGATCATATCGTTTTTGAATCCAAGACTGCCTGTCACTCATGGGACG\n+ATGAGCGCTGGGACAACTTCTGCCTGGTCACACCGAATTGGCAATGTGAACTCCCCGGGCACCCATACAA\n+GGGAAAAGATCCACACGGCTTCATGGTGAAGCAGGAAATCATTGAATACGTCAAAGGCTTTGTTAACTCG\n+TTCAATCCCCCGCTGCGTGAACACACAGCCGTCACCTCCATCACACGTCATGAGGCCGGTGGCTATCGTG\n+TGGTGGCGGGCGGTGAGACCTGGCACACAAAGCATGTGGTCATCGCCTCGGGAGCGTACCAGGATGCGGT\n+GATCCCCGGATATGCGAGTGCTATCGATCCATCAATCTTTCAGGTTCACTCGCAGGATTACCGCAATGCG\n+GCCCAGTTGCCTGAAGGGGCTGTCCTGGTCGTGGGCAGCGGTCAGTCCGGTGCACAGATCGTCGAGGACC\n+TGTTCCTTGAAAAACGCAAGGTCCATCTGTGTGTCGGCTCCGCCCCGCGTGTCTCACGCTTTTACCGTGG\n+CCGTGACGTTGTGGACTGGCTGGCGGATATGCACTTCTATGATCTGACGGTGGATAATCACCCCTTACGG\n+GAAGGGGCGCGGGATAAGACCAACCATTATGTCACCGGCCGCAATGGGGGGCATGACCTTGATCTGCGTC\n+TTTTTGCAAAAGAAGGGATAGGATTGCATGGTACGCTTGAGACAATCCGTGATGAGGTTGCGCATTTTCT\n+TCCAGATCTAAAGCAACATCTCGACGATGCGGACAAGACCAATGCAGACATTAAGAAATCCATTGATGCC\n+TATATTGCTCGCGAAAACATCAATGCACCGACGGAAGCGCCTTACGTACCTGTCTGGCAGCCTGATGGAA\n+GCAACACGCCGCTCGATCTGAAGGCCGCTGGAATCACATCGATCGTCTGGTGCATCGGCTTCCGTCCGAA\n+CTACCGCTGGATCGATGTGCCCGTCTTCAACGGTGCTAACAAGCCGGTCTGGCATCGGGGCGTGACGGAT\n+GCGCCGGGCTTTTATTTTCTTGGTCTGCCATGGCTGCATACATGGGGCTCCGGGCGGTTTTCCGGCATTT\n+CCCGTGATGCTGCGTGGCTGGCCAGCCAGATCACCGGCAAAGACGTGCCCATAGCCTGATCGGAGTATGC\n+GCCATGCTTCCATGGACAACTTATGAAGCGATGTATGATGCGGCACTGAACCAGCCAGAGGAATTCTGGC\n+TCAGTGCGGCGCAGCGTATCACATGGAAGCAGGAGCCTGCGATGGCCTGCCGGGAGCGAACAGACGGTTG\n+GCATGACTGGTTCCCTGACGGCACGCTCAATACCTGCCACAATGCCGTAGACCGGCATGTGGAGAATGGT\n+CGCGGTGAGCAGGTAGCGTTGATCTGGCATTCTTGCGCCACCAAGGAACAGCAGGTCGTGACCTATTGCG\n+AACTGCAGGACAGGGTGGCCGGATTTGCCGGCGGCCTACGCCTGCTCGGAGTGGAGAAAGGCGACCGCGT\n+TCTGATTGCCATGCCGACCATGATCGAGACAGCCATAGCTATGTTGGCATGTGCGCGGATAGGGGCTGTG\n+CATGTTGTGGTTTTTGCCGGTTATGCCGGACCGGAGTTGGCACGACGGATTGATGATGTGGCTCCGAAAG\n+TCATTATCATTGCCAGTTGCAGCTTTCAGGGACAGACGCCTATTCCGTCTGCCCCTGCTCTGAATGATGC\n+ACTTGCTTTGGCAGCGTACCGGCCACAGGCTTGCGTGATTGTGCAACGCGCAGCATGTCGGACATCATTC\n+ATGCCACTGCGGGATCATGATTTCCATACGCTGGAACAGTCCGCGCCTGTAGAGCCCGTCGTGCTACGCT\n+CCGAAGATCCACTCTATATTCTTCACACATCTGGCACGACGGGGCACGCAAAAGGCATTGTGCGTGATAA\n+TGGCGGCCATGCTGTGGTTCTCGCCTTGTCCATGGACGTGATCTACGGCTGCGAACCCGGTGATACCTTC\n' |
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| diff -r 000000000000 -r 735872ff8222 test-data/MRSA0252_trimmed.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MRSA0252_trimmed.fna Mon Dec 12 15:07:38 2016 -0500 |
| [ |
| b'@@ -0,0 +1,217 @@\n+>lcl|NC_002952.2_gene_353 [locus_tag=SAR_RS01765] [location=395237..396418]\n+ATGACGAGAGTCGTATTAGCAGCAGCATACAGGACACCTATTGGCGTTTTTGGAGGTGCGTTTAAAGACG\n+TGCCAGCCTATGATTTAGGTGCGACTTTAATAGAACATATTATTAAAGAGACGGGTTTGAATCCAAGTGA\n+GATTAATGAAGTCATCATCGGTAACGTACTACAAGCAGGACAAGGACAAAATCCAGCACGAATTGCTGCT\n+ATGAAAGGTGGCTTGCCAGAAACAGTACCTGCATTTACAGTGAATAAAGTATGTGGTTCTGGGTTAAAGT\n+CGATTCAATTAGCATATCAATCTATTGTGACTGGTGAAAATGACATCGTGCTAGCTGGCGGTATGGAGAA\n+TATGTCTCAATCACCAATGCTTGTCAACAACAGTCGCTTTGGTTTTAAAATGGGACATCAATCAATGGTT\n+GATAGCATGGTATATGATGGTTTAACAGATGTATTTAATCAATATCATATGGGTATTACTGCTGAAAATT\n+TAGTAGAGCAATATGGTATTTCAAGAGAAGAACAAGATACATTTGCTGTAAACTCACAACAAAAAGCAGT\n+ACGTGCACAGCAAAATGGTGAATTTGATAGTGAAATAGTTCCAGTATCGATTCCTCAACGTAAAGGTGAA\n+CCAATCGTTGTCACTAAGGATGAAGGTGTACGTGAAAATGTATCAGTTGAAAAATTAAGTCGCTTAAGAC\n+CAGCTTTCAAAAAAGACGGTACAGTTACAGCAGGTAATGCATCAGGAATCAATGATGGTGCTGCGATGAT\n+GTTAGTCATGTCAGAAGACAAAGCTAAAGAATTAAATATCGAACCATTGGCAGTGCTTGATGGCTTTGGA\n+AGTCATGGTGTAGATCCTGCTATTATGGGTATTGCCCCAGTTGACGCTGTTGAAAAGGCTTTGAAACGTA\n+GTAAAAAAGAATTAAGTGATATTGATGTATTTGAATTAAATGAAGCATTTGCAGCACAATCATTAGCTGT\n+TGATCGTGAATTAAAATTACCTCCTGAAAAGGTGAATGTTAAAGGTGGCGCTATTGCATTAGGACATCCT\n+ATTGGTGCATCTGGTGCTAGAGTTTTAGTGACATTATTGCATCAACTGAATGATGAAGTTGAAACTGGTT\n+TAACATCATTGTGTATTGGTGGCGGTCAAGCTATCGCTGCAGTTGTATCAAAGTATAAATAA\n+>lcl|NC_002952.2_gene_478 [locus_tag=SAR_RS02395] [location=514251..515807]\n+TTTTATGGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGA\n+ACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATA\n+AGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGA\n+AAGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACC\n+AAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCC\n+TACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGAT\n+GAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGA\n+CGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTT\n+ATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAA\n+CCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGT\n+GAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGT\n+GCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTG\n+TTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAA\n+GGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACG\n+CGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAA\n+AGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGC\n+AACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAA\n+GGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACA\n+AAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAAC\n+TCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCT\n+TGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCT\n+AGCCGTCGAAGGTGGGACAAATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTG\n+GATCACCTCCTTTCTAA\n+>lcl|NC_002952.2_gene_534 [locus_tag=SAR_RS02675] [location=559978..561534]\n+TTTTATGGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGA\n+ACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATA\n+AGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGA\n+AAGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACC\n+AAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCC\n+TACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGAT\n+GAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGA\n+CGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTT\n+ATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAA\n+CCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGT\n+GAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGT\n+GCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTG\n+TTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC'..b'+TACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGAT\n+GAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGA\n+CGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTT\n+ATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAA\n+CCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGT\n+GAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGT\n+GCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTG\n+TTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAA\n+GGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACG\n+CGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAA\n+AGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGC\n+AACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAA\n+GGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACA\n+AAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAAC\n+TCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCT\n+TGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCT\n+AGCCGTCGAAGGTGGGACAAATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTG\n+GATCACCTCCTTTCTAA\n+>lcl|NC_002952.2_gene_2347 [locus_tag=SAR_RS11775] [location=complement(2335734..2337289)]\n+TTGTATGGAGAGTTTGATCCTGGCCCATGATGAACGCTGGCGGCGTGTCCTATACATGCCAGTCGAGCGA\n+ACGGACGAAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAA\n+GACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAA\n+AGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACCA\n+AGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCT\n+ACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATG\n+AAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGAC\n+GGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTA\n+TCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAAC\n+CGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTG\n+AAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTG\n+CGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGT\n+TAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAG\n+GTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGC\n+GAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAAA\n+GTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCA\n+ACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAG\n+GTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAA\n+AGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACT\n+CGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCTT\n+GTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCTA\n+GCCGTCGAAGGTGGGACAAATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGG\n+ATCACCTCCTTTCTAA\n+>lcl|NC_002952.2_gene_2842 [locus_tag=SAR_RS14265] [location=complement(2805880..2806821)]\n+ATGAAAGAGAAAATTGTCATTGCATTAGGCGGTAATGCGATACAGACAAAAGAAGCAACAGCTGAAGCAC\n+AACAAACAGCTATTAGACGTGCGATGCAAAACCTTAAACCTTTATTTGATTCACCAGCGCGTATTGTCAT\n+TTCACATGGTAATGGTCCACAAATTGGAGGTTTATTAATCCAACAAGCTAAATCGAACAGTGACACAACG\n+CCGGCAATGCCATTGGATACTTGTGGTGCAATGTCACAAGGTATGATAGGCTATTGGTTGGAAACTGAAA\n+TCAATCGCATTTTAACTGAAATGAATAGTGATAGAACTGTAGGCACAATCGTAACACGTGTGGAAGTAGA\n+TAAAGATGATCCACGATTTGATAACCCAACTAAACCAATTGGTCCTTTTTATACGAAAGAAGAAGTTGAA\n+GAATTACAAAAAGAACAGCCAGGCTCAGTCTTTAAAGAAGATGCAGGACGTGGTTATAGAAAAGTAGTTG\n+CGTCACCACTACCTCAATCTATACTAGAACACCAGTTAATTCGAACTTTAGCAGACGGTAAAAATATTGT\n+CATTGCATGCGGTGGTGGCGGTATTCCAGTTATAAAAAAAGAAAATACCTATGAAGGTGTTGAAGCGGTT\n+ATAGATAAAGATTTTGCTAGTGAGAAATTAGCAACGCTGATTGAAGCAGATACCTTAATGATTCTTACGA\n+ATGTAGAAAATGTATTTATTAACTTTAATGAACCTAATCAACAACAAATCGATGATATTGATGTAGCAAC\n+ACTGAAAAAATACGCGGCACAAGGTAAGTTTGCGGAAGGATCGATGTTGCCAAAAATAGAAGCTGCGATA\n+CGATTTGTTGAAAGTGGGGAAAACAAAAAAGTTATCATTACCAATTTAGAGCAGGCATACGAAGCTTTGA\n+TTGGTAATAAAGGTACACACATTCACATGTAG\n' |
| b |
| diff -r 000000000000 -r 735872ff8222 test-data/output_list.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_list.txt Mon Dec 12 15:07:38 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +abaumannii abaumannii_2 achromobacter aeromonas afumigatus aphagocytophilum arcobacter bcc bcereus bhampsonii bhenselae bhyodysenteriae bintermedia blicheniformis bordetella borrelia bpilosicoli bpseudomallei brachyspira bsubtilis calbicans campylobacter cbotulinum cconcisus cdifficile cdiphtheriae cfetus cfreundii cglabrata chelveticus chlamydiales chyointestinalis cinsulaenigrae ckrusei clanienae clari cmaltaromaticum cronobacter csepticum csinensis csputorum ctropicalis cupsaliensis ecloacae ecoli ecoli_2 efaecalis efaecium fpsychrophilum hcinaedi hinfluenzae hparasuis hpylori hsuis kkingae koxytoca kpneumoniae kseptempunctata leptospira leptospira_2 leptospira_3 lmonocytogenes lsalivarius mabscessus magalactiae mbovis mcatarrhalis mhaemolytica mhyorhinis mmassiliense mplutonius neisseria orhinotracheale otsutsugamushi pacnes paeruginosa pfluorescens pgingivalis plarvae pmultocida_multihost pmultocida_rirdc ppentosaceus ranatipestifer sagalactiae saureus scanis sdysgalactiae senterica sepidermidis sgallolyticus shaemolyticus shominis sinorhizobium slugdunensis smaltophilia soralis spneumoniae spseudintermedius spyogenes ssuis sthermophilus sthermophilus_2 streptomyces suberis szooepidemicus taylorella tenacibaculum tvaginalis vcholerae vibrio vparahaemolyticus vtapetis vvulnificus wolbachia xfastidiosa yersinia ypseudotuberculosis yruckeri |
| b |
| diff -r 000000000000 -r 735872ff8222 test-data/output_longlist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_longlist.txt Mon Dec 12 15:07:38 2016 -0500 |
| b |
| @@ -0,0 +1,118 @@ +abaumannii Oxf_gltA Oxf_gyrB Oxf_gdhB Oxf_recA Oxf_cpn60 Oxf_gpi Oxf_rpoD +abaumannii_2 Pas_cpn60 Pas_fusA Pas_gltA Pas_pyrG Pas_recA Pas_rplB Pas_rpoB +achromobacter nusA rpoB eno gltB lepA nuoL nrdA +aeromonas gyrB groL gltA metG ppsA recA +afumigatus ANX4 BGT1 CAT1 LIP MAT1_2 SODB ZRF2 +aphagocytophilum pheS glyA fumC mdh sucA dnaN atpA +arcobacter aspA atpA glnA gltA glyA pgm tkt +bcc atpD gltB gyrB recA lepA phaC trpB +bcereus glp gmk ilv pta pur pyc tpi +bhampsonii Bha_adh Bha_est Bha_gdh Bha_glpK Bha_pgm Bha_thi +bhenselae _16S batR ftsZ gltA groEL nlpD ribC rpoB +bhyodysenteriae Bhy_adh Bhy_alp Bhy_est Bhy_gdh Bhy_glpK Bhy_pgm Bhy_thi +bintermedia Bin_adh Bin_alp Bin_est Bin_gdh Bin_glpK Bin_pgm Bin_thi +blicheniformis adk ccpA recF rpoB spo0A sucC +bordetella adk fumC glyA tyrB icd pepA pgm +borrelia clpA clpX nifS pepX pyrG recG rplB uvrA +bpilosicoli Bpi_adh Bpi_alp Bpi_est Bpi_gdh Bpi_glpK Bpi_pgm Bpi_thi +bpseudomallei ace gltB gmhD lepA lipA narK ndh +brachyspira Bra_adh Bra_alp Bra_est Bra_gdh Bra_glp Bra_pgm Bra_thi +bsubtilis glpF ilvD pta purH pycA rpoD tpiA +calbicans AAT1a ACC1 ADP1 MPIb SYA1 VPS13 ZWF1b +campylobacter aspA glnA gltA glyA pgm tkt uncA +cbotulinum aroE mdh aceK oppB rpoB recA hsp +cconcisus Cco_aspA Cco_atpA Cco_glnA Cco_gltA Cco_glyA Cco_ilvD Cco_pgm +cdifficile adk atpA dxr glyA recA sodA tpi +cdiphtheriae atpA dnaE dnaK fusA leuA odhA rpoB +cfetus Cfe_aspA Cfe_glnA Cfe_gltA Cfe_glyA Cfe_pgm Cfe_tkt Cfe_uncA +cfreundii aspC clpX fadD mdh arcA dnaG lysP +cglabrata FKS LEU2 NMT1 TRP1 UGP1 URA3 +chelveticus Che_aspA Che_atpA Che_glnA Che_gltA Che_glyA Che_pgm Che_tkt +chlamydiales gatA oppA hflX gidA enoA hemN fumC +chyointestinalis Chy_aspA Chy_atpA Chy_glnA Chy_gltA Chy_glyA Chy_pgm Chy_tkt +cinsulaenigrae Cin_aspA Cin_atpA Cin_glnA Cin_glyA Cin_pgi Cin_pgm Cin_tkt +ckrusei HIS3 LEU2 NMT1 TRP1 ADE2 LYS2D +clanienae Cln_aspA Cln_atpA Cln_glnA Cln_gltA Cln_glyA Cln_pgm Cln_tkt +clari Cla_adk Cla_atpA Cla_glnA Cla_glyA Cla_pgi Cla_pgm Cla_tkt +cmaltaromaticum dapE ddlA glpQ ilvE leuS pyc pyrE +cronobacter atpD fusA glnS gltB gyrB infB pps +csepticum ddl dnaK glpK groEL gyrA recA tpi +csinensis Actin Cox1 Cox3 Ef_1a Its1 Nad4 Nad5 Tubulin +csputorum Csp_aspA Csp_atpA Csp_glnA Csp_gltA Csp_glyA Csp_pgm Csp_tkt +ctropicalis ICL1 MDR1 SAPT2 SAPT4 XYR1 ZWF1a +cupsaliensis Cup_adk Cup_aspA Cup_atpA Cup_glnA Cup_glyA Cup_pgi Cup_tkt +ecloacae dnaA fusA gyrB leuS pyrG rplB rpoB +ecoli adk fumC gyrB icd mdh purA recA +ecoli_2 dinB icdA pabB polB putP trpA trpB uidA +efaecalis gdh gyd pstS gki aroE xpt yqiL +efaecium atpA ddl gdh purK gyd pstS adk +fpsychrophilum atpA dnaK fumC gyrB murG trpB tuf +hcinaedi _23S_rRNA ppa aspA aroE atpA tkt cdtB +hinfluenzae adk atpG frdB fucK mdh pgi recA +hparasuis atpD infB mdh rpoB _6pgd g3pd frdB +hpylori atpA efp mutY ppa trpC ureI yphC +hsuis atpA efp mutY ppa trpC ureAB yphC +kkingae abcZ adk aroE cpn60 gdh recA +koxytoca gapA infB mdh pgi phoE rpoB tonB +kpneumoniae gapA infB mdh pgi phoE rpoB tonB +kseptempunctata cox1 rnl +leptospira glmU pntA sucA tpiA pfkB mreA caiB +leptospira_2 adk_2 glmU_2 icdA_2 lipL32_2 lipL41_2 mreA_2 pntA_2 +leptospira_3 adk_3 icdA_3 lipL32_3 lipL41_3 rrs2_3 secY_3 +lmonocytogenes abcZ bglA cat dapE dat ldh lhkA +lsalivarius pstB rpsB nrdB rpoA parB +mabscessus Mab_argH Mab_cya Mab_gnd Mab_murC Mab_pta Mab_purH Mab_rpoB +magalactiae dnaA gltX gyrB metS tufA +mbovis adh1 gltX gpsA gyrB pta2 tdk tkt +mcatarrhalis abcZ adk efp fumC glyBETA mutY ppa trpE +mhaemolytica adk aroE deoD gapDH gnd mdh zwf +mhyorhinis dnaA rpoB gyrB gltX adk gmk +mmassiliense Mma_argH Mma_cya Mma_gnd Mma_murC Mma_pta Mma_purH Mma_rpoB +mplutonius argE galK gbpB purR +neisseria abcZ adk aroE fumC gdh pdhC pgm +orhinotracheale adk aroE fumC gdhA mdh pgi pmi +otsutsugamushi gpsA mdh nrdF nuoF ppdK sucB sucD +pacnes aroE atpD gmk guaA lepA sodA tly CAMP2 +paeruginosa acs aro gua mut nuo pps trp +pfluorescens glnS gyrB ileS nuoD recA rpoB rpoD +pgingivalis ftsQ gpdxJ hagB mcmA pepO pga recA +plarvae glpF sigF glpT Natrans rpoB ftsA clpC +pmultocida_multihost adk aroA deoD gdhA g6pd mdh pgi +pmultocida_rirdc adk est pmi zwf mdh gdh pgi +ppentosaceus gyrB pyc pgm leuS glnA dalR pgI +ranatipestifer dnaB groEL gyrA mdh gluD gpi rpoB +sagalactiae adhP pheS atr glnA sdhA glcK tkt +saureus arcC aroE glpF gmk pta tpi yqiL +scanis gki gtr murI mutS recP xpt yqiZ +sdysgalactiae gki gtr murI mutS recP xpt atoB +senterica aroC dnaN hemD hisD purE sucA thrA +sepidermidis arcC aroE gtr mutS pyrR tpiA yqiL +sgallolyticus aroE glgB nifS p20 tkt trpD uvrA +shaemolyticus arcC SH_1200 hemH leuB SH1431 cfxE Ribose_ABC +shominis arcC glpK gtr pta tpiA tuf +sinorhizobium asd edd gap glnD gnd nuoE1 ordL2 recA sucA zwf +slugdunensis aroE dat ddl gmk ldh recA yqiL +smaltophilia atpD gapA guaA mutM nuoD ppsA recA +soralis aroE ddl gdh gki hexB recP xpt +spneumoniae aroE gdh gki recP spi xpt ddl +spseudintermedius ack cpn60 fdh pta purA sar tuf +spyogenes gki gtr murI mutS recP xpt yqiL +ssuis aroA cpn60 dpr gki mutS recA thrA +sthermophilus ddlA glcK proA ptsI serB tkt +sthermophilus_2 carB clpX dnaA murC murE pepN pepX pyrG recA rpoB +streptomyces _16S atpD gyrB recA rpoB trpB +suberis arcC ddl gki recP tdk tpi yqiL +szooepidemicus arcC nrdE proS spi tdk tpi yqiL +taylorella gltA gyrB fh shmt tyrB adk txn +tenacibaculum atpA dnaK glyA gyrB infB rlmN tgt +tvaginalis TRYP GLUT FT2A ALTS DMRP SHMT M6PI +vcholerae adk gyrB mdh metE pntA purM pyrC +vibrio gyrB pyrH recA atpA +vparahaemolyticus dnaE gyrB recA dtdS pntA pyrC tnaA +vtapetis atpA fstZ gapA hsp60 pyrH rctB recA rpoA rpoD topA +vvulnificus glp gyrB mdh metG purM dtdS lysA pntA pyrC tnaA +wolbachia gatB coxA hcpA ftsZ fbpA +xfastidiosa leuA petC malF cysG holC nuoL gltT +yersinia aarF dfp galR glnS hemA rfaE speA +ypseudotuberculosis adk argA aroA glnA thrA tmk trpE +yruckeri glnA gyrB dnaJ thrA hsp60 recA |
| b |
| diff -r 000000000000 -r 735872ff8222 test-data/output_mincov100.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_mincov100.txt Mon Dec 12 15:07:38 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) |
| b |
| diff -r 000000000000 -r 735872ff8222 test-data/output_minid100.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_minid100.txt Mon Dec 12 15:07:38 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) |
| b |
| diff -r 000000000000 -r 735872ff8222 test-data/output_mrsa.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_mrsa.txt Mon Dec 12 15:07:38 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) |
| b |
| diff -r 000000000000 -r 735872ff8222 test-data/output_noresults.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_noresults.txt Mon Dec 12 15:07:38 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ + - - |
| b |
| diff -r 000000000000 -r 735872ff8222 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 12 15:07:38 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mlst" version="2.6"> + <repository changeset_revision="53b0a618e1a7" name="package_mlst_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |