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Commit message:
planemo upload commit 132092ff7fe1c4810d1221054419389180b81657 |
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getmlst.pl getmlst.xml test-data/mlst_database_test.fasta test-data/mlst_definitions_test.tabular |
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| diff -r 000000000000 -r c2e910327131 getmlst.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getmlst.pl Fri Nov 17 11:49:10 2017 -0500 |
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| @@ -0,0 +1,34 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use Cwd; +use File::Copy; + +my ($mlst_db, $mlst_defs, $species) = @ARGV; + +$species =~ s/__pd__/#/ig; + +my $command = "getmlst.py --species '$species'"; + +my $rv = system($command); + +if ($rv == 0) +{ + #need to find output files in the dir + my $cur_dir = getcwd(); + + foreach my $file (<$cur_dir/*>) + { + if ($file =~ /\.fasta$/) + { + move($file, $mlst_db); + } + elsif ($file =~/\.txt$/) + { + move($file, $mlst_defs); + } + } +} +$rv = $rv >> 8; +exit $rv; |
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| diff -r 000000000000 -r c2e910327131 getmlst.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getmlst.xml Fri Nov 17 11:49:10 2017 -0500 |
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| @@ -0,0 +1,101 @@ +<tool id="getmlst" name="getmlst" version="0.1.4.1"> + <description>Download MLST datasets by species from pubmlst.org</description> + <requirements> + <requirement type="package" version="0.1.4.6">srst2</requirement> + </requirements> + <stdio> + <exit_code range="2" level="fatal" description="Please be more specific."/> + <exit_code range="1" level="fatal" description="No species matched your query."/> + </stdio> + <command><![CDATA[ + $__tool_directory__/getmlst.pl $mlst_db $mlst_defs '$species' + ]]></command> + <inputs> + <param name="species" type="text" label="The name of the genus, or genus and species that you want to download." help="Please note you will receive an error if multiple results are returned."/> + </inputs> + <outputs> + <data format="fasta" name="mlst_db" label="MLST Database"/> + <data format="tabular" name="mlst_defs" label="MLST Definitions"/> + </outputs> + <tests> + <test> + <param name="species" value="Listeria monocytogenes"/> + <output name="mlst_db" file="mlst_database_test.fasta" ftype="fasta"/> + <output name="mlst_defs" file="mlst_definitions_test.tabular" ftype="tabular"/> + </test> + </tests> + <help> + +**GetMLST** + +GetMLST_ downloads MLST datasets from pubmlst.org. + +Data is downloaded for a species determined by the users + + - profiles (maps STs to allele numbers) + - numbered sequences for each locus in the scheme + +In addition, the alleles are concatenated together for use with SRST2. + +.. _`GetMLST`: https://github.com/katholt/srst2 + +----- + +**What it does** + +Searches a database for a given organism and returns the MLST Database(fasta) and MLST Definitions(tabular). + +**Usage** + +Enter the genus and species of the organism to search and press Execute + +**Tips** + +1. To produce a list of all species avaialble for a specific genus, enter the genus name and press "Execute". + + - *Helicobacter* will not generate MLST Database or MLST Definition files and an error will occur however the following output will be generated: + + - *The following 3 species match your query, please be more specific:* + - Helicobacter cinaedi + - Helicobacter pylori + - Helicobacter suis + + - + +2. To return a list of all species available from a database leave the name blank and press "Execute". + + - Leaving the text field blank will not generate MLST Database or MLST Definition files and an error will occur however the following output will be generated: + + - *The following 114 species match your query, please be more specific:* + - Achromobacter spp. + - Acinetobacter baumannii#1 + - Acinetobacter baumannii#2 + - Aeromonas spp. + - Anaplasma phagocytophilum + - Arcobacter spp. + - Aspergillus fumigatus + - Bacillus cereus + - Bacillus licheniformis + - Bacillus subtilis + - Bifidobacterium + - Bordetella spp. + - Borrelia spp. + - Brachyspira hampsonii + - Brachyspira hyodysenteriae + - Brachyspira intermedia + - Brachyspira pilosicoli + - Brachyspira spp. + - Burkholderia cepacia complex + - Burkholderia pseudomallei + - Campylobacter concisus/curvus + - Campylobacter fetus + - Campylobacter helveticus + - Campylobacter hyointestinalis + - ... + + </help> + + <citations> + <citation type="doi">10.1186/s13073-014-0090-6</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r c2e910327131 test-data/mlst_database_test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mlst_database_test.fasta Fri Nov 17 11:49:10 2017 -0500 |
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| b'@@ -0,0 +1,15049 @@\n+>abcZ_1\n+AAATCGACGAACAGAATGCGTATAGGACTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGTCGTTTCACTAGTGACTTAGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_2\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGTCGTTTCACTAGTGACTTAGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_3\n+AAATCGACGAACAGAATGCGTATAGGACTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGTCGCAATGATGGCGAAATGCTTAGTCGTTTCACTAGTGACTTAGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCAACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATTGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_4\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGCCGCTTCACTAGTGACTTGGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGCTA\n+>abcZ_5\n+AAATCAACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCGATTCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGCCGCTTCACTAGCGACTTAGATAAT\n+ATTTCCAATACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCAATTATTATTGCGACAGTGATTATTCGAAAAGCACGTAAATTCGTTGAT\n+GTTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGACAA\n+AAAATCATTATCACAAATGGTTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTATAAAGGGCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_6\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCGATTCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGTCGTTTTACTAGTGACTTAGATAAT\n+ATTTCCAATACACTAAACCAAGCATTGATCCAGGTGCTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTTTAATATCT\n+GCTCCATTTGCGATTATTATTGCAACAGTGATTATTCGAAAAGCACGTAAATTCGTTGAT\n+GTTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGACAA\n+AAAATCATTATCACAAATGGTTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTATAAAGGGCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCACTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_7\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCGATTCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGCCGCTTCACTAGTGACTTAGATAAT\n+ATTTCCAATACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCAATTATTATTGCGACAGTGATTATTCGAAAAGCACGTAAATTCGTTGAT\n+GTTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGACAA\n+AAAATCATTATCACAAATGGTTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTATAAAGGGCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_8\n+AAATCGACGAACAGAATGCGT'..b'TCTTCGGAAGATAAG\n+AAAAAACTGGAAAGCGGCGAAACGGTTAGCAAGAAAATAGATAATCGATTCAATAGAGAA\n+ATGACGATTGTTTATGTGCCGATTATGGATGGTGATAAATTTGTCGGTTCTATCGTGCTG\n+AATTCACCTATTAGCGGGACCGAGCAAGTAATTGGTACTATTAATCGTTACATGTTTTAT\n+ACTATTTTACTTTCCATAACCGTAGCACTTATTCTTAGTGCGATTTTGTCCAAACTACAA\n+GTGAATAGAATCAACAAACTACGAGCAGCGACGAAAGATGTTATTCAAGGCAACTACAAA\n+GCCAGACTAAAAGAAAATAACTTTGATGAAATTGGCGCGCTTGCGATTGATTTCAATAAG\n+ATGACTCAAACACTGGAAATTTCTCAAGAAGAAATTGAAAGACAAGAAAAACGGCGCCGT\n+>lhkA_180\n+TATCCAACACAAATGGACCAGCCTCTACCTAAAGACTTTTCGATTTCTTCGGAAGATAAG\n+AAAAAACTGGAAAGCGGCGAAACGGTTAGCAAGAAAATAGATAATCGATTCAATAGAGAA\n+ATGACGATTGTTTATGTGCCGATTATGGATGGTGATAAATTTGTCGGTTCTATCGTGCTG\n+AATTCACCTATTAGCGGGACCGAGCAAGTAATTGGTACGATTAATCGTTATATGTTCTAT\n+ACTATTTTACTCTCCATAACAGTAGCACTTATTCTTAGTGCGATATTGTCCAAACTACAA\n+GTGAATCGAATCAACAAACTACGAGCAGCGACGAAAGATGTTATTCAAGGCAACTACAAA\n+GCCAGACTAAAAGAAAATAACTTTGATGAAATTGGTGCGCTTGCGATTGATTTCAATAAG\n+ATGACTCAAACACTGGAAATTTCTCAAGAAGAAATTGAAAGACAAGAAAAACGGCGCCGT\n+>lhkA_181\n+TACCCAACCCAGCTAAATCAGCCATTACCCAAGGACTTCTCTATTTCATCTGATGATAAG\n+AAAAAATTAGAAAGTGGCGAAACGGTAAGTAAAAAGATTGATAATCGTTTTAATAGAGAA\n+ATGACGATTGTGTATGTTCCGATTATGGATGGCAGCAAATTTGTTGGTTCAATCGTGCTG\n+AATTCGCCGATAAGCGGCACCCAGCAAGTCATAGGTACAATTAATCGTTATATGTTCTAC\n+ACTATTTTGCTTTCTATCACTGTGGCACTTATCCTTAGCGCGATTTTATCCAAGCTGCAA\n+GTCAATCGGATTAATAAACTGCGTGCTGCCACCAAAGATGTTATTCAAGGTAATTACAAA\n+GCCAGACTAAAAGAAAATAACTTCGATGAGATCGGCGCGCTTGCTATTGATTTCAATAAA\n+ATGACGCAAACACTCGAAACGTCCCAAGAAGAAATTGAACGTCAAGAAAAACGGCGTCGT\n+>lhkA_182\n+TATCCAACCCAGCTAAATCAGCCATTACCCAAGGACTTCTCTATTTCATCTGATGATAAG\n+AAAAAATTAGAAAGTGGCGAAACGGTAAGTAAAAAGATTGATAATCGTTTTAATAGAGAA\n+ATGACGATTGTGTATGTTCCGATTATGGATGGCAGCAAATTTGTTGGTTCAATCGTGCTG\n+AATTCGCCGATAAGCGGCACCCAGCAAGTCATAGGTACAATTAATCGTTATATGTTCTAC\n+ACTATTTTGCTTTCTATCACTGTGGCACTTATCCTTAGCGCGATTTTATCCAAGCTGCAA\n+GTCAATCGGATTAATAAACTGCGTGCTGCCACCAAAGATGTTATTCAAGGTAATTACAAA\n+GCCAGACTAAAAGAAAATAACTTCGATGAGATCGGCGCGCTTGCTATTGATTTCAATAAA\n+ATGACGCAAACACTCGAAACGTCCCAAGAAGAAATTGAACGTCAAGAAAAACGGCGTCGT\n+>lhkA_183\n+ATTTATCCGAGTTCAAGTCGTCCACTCCCACCTGATTTTAAAATTTCAGACGCGGATATG\n+AAAAAATTAAAAAAAGGTGAAACCGTGACAATTAAAGTGGACAGTCGTTTTAACCAGGGA\n+ATGTCTGTCGTTTATGTGCCTATTATGAACGGGGAAAGCTATTTGGGTGCGGTTATTTTA\n+AATGCTCCGATTAGTGGGACGGAAAAAGTGGTTGGGACGATTAACCAATATATGTTCTAT\n+GCGATTCTGATTTCCATTCTGGTAGCTTTGATTTTAAGTTTCCTAATGTCGAAGCTTCAA\n+GTCAATCGAATTAATAAACTGCGGGACGCAACCAAGCGTGTGACGCGCGGGGATTATGAG\n+ACGCGGTTAAAAGAAAATAAGGTGGATGAAATTGGCGAACTGGCGCACGATTTTAACCGT\n+ATGACGGAAAATTTAGCGGAATCCCGCGAAGAAATTGAACGTCAAGAGCGCCGCAGAAGA\n+>lhkA_184\n+TATCCAACACAGATGAATCAGCCGTTACCAAAGGATTTCTCTATTTCTTCGGATGATAAG\n+AAAAAGCTTGAAAGTGGCGAAACAGTTAGTAAGAAAATAGATAATCGCTTTAATAAAGAA\n+ATGACAATTGTGTACCTCCCAATAATGAATGGCGACAAATTTGTCGGTTCTATCGTGCTC\n+AATTCACCTATTAGCGGTACGAAGCAAGTAATTGGTACGATTAACCGCTATATGTTCTAC\n+ACTATTTTACTTTCTATAACGGTAGCACTTATTCTTAGCGCAATCTTGTCCAAACTACAA\n+GTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGGCAATTACAAA\n+GCTCGATTGAAGGAAAATAATTTTGATGAAATTGGTGCACTTGCCATTGATTTCAATAAA\n+ATGACACAAACCCTTGAAACATCTCAAGAAGAAATAGAACGACAAGAGAAGCGGAGACGC\n+>lhkA_185\n+TATCCAACACAGATGAATCAGCCGTTACCAAAGGATTTCTCTATTTCTTCGGATGATAAG\n+AAAAAACTTGAAAGTGGCGAAACAGTTAGTAAGAAAATAGATAATCGCTTTAATAAAGAA\n+ATGACAATTGTGTACGTCCCAATAATGAATGGCGACAAATTTGTCGGTTCTATCGTGCTC\n+AATTCACCTATTAGCGGTACGGAGCAAGTAATTGGTACGATTAACCGCTATATGTTCTAC\n+ACTATTTTACTTTCTATAACGGTAGCACTTATTCTTAGCGCAATCTTGTCCAAACTACAA\n+GTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGACAATTACAAA\n+GCTCGATTGAAGGAAAATAATTTTGATGAAATTGGTGCACTTGCCATTGATTTCAATAAA\n+ATGACACAAACCCTTGAAACATCTCAAGAAGAAATAGAACGACAAGAGAAGCGGAGACGC\n+>lhkA_186\n+TATCCAACACAGATGAATCAGCCTTTACCTAAGGATTTCTCTATTTCTGCGGATGATAAG\n+AAAAAGCTTGAAAGTGGTGAAACGGTTAGTAAAAAAATAGATAATCGCTTTAACAAAGAA\n+ATGACAATTGTGTACGTCCCAATAATGAATGGCGATAAATTTGTCGGTTCTATCGTGCTG\n+AATTCACCCATTAGCGGTACGGAGCAAGTAATTGGCACGATTAACCGCTATATGTTCTAC\n+ACTATTTTACTTTCTATAACGGTAGCACTTATTCTTAGCGCAATCTTGTCCAAACTACAA\n+GTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGGCAATTACAAC\n+GCTCGCTTGAAGGAAAATAATTTTGATGAAATTGGTGCACTCGCCATTGATTTCAATAAA\n+ATGACACAAACCCTTGAAACATCTCAAGAAGAAATTGAACGACAAGAGAAACGGAGACGC\n' 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| diff -r 000000000000 -r c2e910327131 test-data/mlst_definitions_test.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mlst_definitions_test.tabular Fri Nov 17 11:49:10 2017 -0500 |
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