# HG changeset patch # User iuc # Date 1539603708 14400 # Node ID 68cdb40ff91c4051457681caccc66bd42068676a # Parent 253b7a1cf87eae12f53c9cc76c5cbe1e4c296af9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67 diff -r 253b7a1cf87e -r 68cdb40ff91c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 15 07:41:48 2018 -0400 @@ -0,0 +1,26 @@ + + 2.15.1 + + + + mlst + + + + + mlst --version + + + + + + @UNPUBLISHED{Seemann2016, + author = "Seemann T", + title = "MLST: Scan contig files against PubMLST typing schemes", + year = "2016", + url = {https://github.com/tseemann/mlst} + } + + + + diff -r 253b7a1cf87e -r 68cdb40ff91c mlst.xml --- a/mlst.xml Mon Feb 12 05:18:20 2018 -0500 +++ b/mlst.xml Mon Oct 15 07:41:48 2018 -0400 @@ -1,28 +1,60 @@ - - - mlst - + + Scans genomes against PubMLST schemes. + + macros.xml + + + + + + + - mlst --version + "$report" ]]> - + @@ -31,46 +63,242 @@ - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + settings['advanced'] == "advanced" and settings['novel'] + - + - + - + - + - + - - + + - + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -95,7 +323,7 @@ **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. +If you choose to manually set the MLST scheme, it will print a fixed tabular output with a heading containing allele names specific to that scheme (adjustable with **Include allele header**). To view a list of schemes, use the MLST List tool. :: @@ -103,30 +331,27 @@ 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 | -+--------+---------------------------+ ++--------+---------------------------------------+ +| Symbol | Meaning | ++========+=======================================+ +| n | Exact intact allele | ++--------+---------------------------------------+ +| ~n | Novel full length allele similar to n | ++--------+---------------------------------------+ +| n? | Partial match to known allele | ++--------+---------------------------------------+ +| n,m | Multiple alleles | ++--------+---------------------------------------+ +| *-* | Allele missing | ++--------+---------------------------------------+ + +Setting **Output novel alleles** to true will produce an additional **novel_alleles.fasta** file containing the novel alleles. Galaxy wrapper maintained by Simon Gladman. ]]> - - - @UNPUBLISHED{Seemann2016, - author = "Seemann T", - title = "MLST: Scan contig files against PubMLST typing schemes", - year = "2016", - note = "https://github.com/tseemann/mlst"} - - + diff -r 253b7a1cf87e -r 68cdb40ff91c mlst_list.xml --- a/mlst_list.xml Mon Feb 12 05:18:20 2018 -0500 +++ b/mlst_list.xml Mon Oct 15 07:41:48 2018 -0400 @@ -1,9 +1,10 @@ - - - mlst - - - mlst --version + + Lists available schemes for the MLST tool. + + macros.xml + + + "$report" @@ -47,13 +48,5 @@ ]]> - - - @UNPUBLISHED{Seemann2016, - author = "Seemann T", - title = "ABRicate: mass screening of contigs for antiobiotic resistance genes", - year = "2016", - note = "https://github.com/tseemann/abricate"} - - + diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/MRSA0252_trimmed_novel.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MRSA0252_trimmed_novel.fna Mon Oct 15 07:41:48 2018 -0400 @@ -0,0 +1,18 @@ +>lcl|NC_002952.2_gene_353 [locus_tag=SAR_RS01765] [location=395237..396418] +ATGACGAGAGTCGTATTAGCAGCAGCATACAGGACACCTtaaccCGTTTTTGGAGGTGCGTTTAAAGACG +TGCCAGCCTATGATTTAGGTGCGACTTTAATAGAACATAaaATTAAAGAGACGGGTTTGAATCCAAGTGA +GATTAATGAAGTCATCATCGGTAACGTACTACAAGCAGGACAAGGACAAAATCCAGCACGAATTGCTGCT +ATGAAAGGTGGCTTGCCAGAAACAGTACCTGCATTTACAGTGAATAAAGTATGTGGTTCTGGGTTAAAGT +CGATTCAATTAGCATATCAATCTATTGTGACTGGTGAAAATGACATCGTGCTAGCTGGCGGTATGGAGAA +TATGTCTCAATCACCAATGCTTGTCAACAACAGTCGCTTTGGTTTTAAAATGGGACATCAATCAATGGTT +GATAGCATGGTATATGATGGTTTAACAGATGTATTTAATCAATATCATATGGGTATTACTGCTGAAAATT +TAGTAGAGCAATATGGTATTTCAAGAGAAGAACAAGATACATTTGCTGTAAACTCACAACAAAAAGCAGT +ACGTGCACAGCAAAATGGTGAATTTGATAGTGAAATAGTTCCAGTATCGATTCCTCAACGTAAAGGTGAA +CCAATCGTTGTCACTAAGGATGAAGGTGTACGTGAAAATGTATCAGTTGAAAAATTAAGTCGCTTAAGAC +CAGCTTTCAAAAAAGACGGTACAGTTACAGCAGGTAATGCATCAGGAATCAATGATGGTGCTGCGATGAT +GTTAGTCATGTCAGAAGACAAAGCTAAAGAATTAAATATCGAACCATTGGCAGTGCTTGATGGCTTTGGA +AGTCATGGTGTAGATCCTGCTATTATGGGTATTGCCCCAGTTGACGCTGTTGAAAAGGCTTTGAAACGTA +GTAAAAAAGAATTAAGTGATATTGATGTATTTGAATTAAATGAAGCATTTGCAGCACAATCATTAGCTGT +TGATCGTGAATTAAAATTACCTCCTGAAAAGGTGAATGTTAAAGGTGGCGCTATTGCATTAGGACATCCT +ATTGGTGCATCTGGTGCTAGAGTTTTAGTGACATTATTGCATCAACTGAATGATGAAGTTGAAACTGGTT +TAACATCATTGTGTATTGGTGGCGGTCAAGCTATCGCTGCAGTTGTATCAAAGTATAAATAA diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_mincov100.txt --- a/test-data/output_mincov100.txt Mon Feb 12 05:18:20 2018 -0500 +++ b/test-data/output_mincov100.txt Mon Oct 15 07:41:48 2018 -0400 @@ -1,1 +1,1 @@ -saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) +MRSA0252_trimmed.fna saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_minid100.txt --- a/test-data/output_minid100.txt Mon Feb 12 05:18:20 2018 -0500 +++ b/test-data/output_minid100.txt Mon Oct 15 07:41:48 2018 -0400 @@ -1,1 +1,1 @@ -saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) +MRSA0252_trimmed.fna saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_mrsa.txt --- a/test-data/output_mrsa.txt Mon Feb 12 05:18:20 2018 -0500 +++ b/test-data/output_mrsa.txt Mon Oct 15 07:41:48 2018 -0400 @@ -1,1 +1,1 @@ -saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) +MRSA0252_trimmed.fna saureus 36 arcC(2) aroE(2) glpF(2) gmk(2) pta(3) tpi(3) yqiL(2) diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_mrsa_exclude.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_mrsa_exclude.txt Mon Oct 15 07:41:48 2018 -0400 @@ -0,0 +1,1 @@ +MRSA0252_trimmed.fna - - diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_mrsa_legacy.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_mrsa_legacy.txt Mon Oct 15 07:41:48 2018 -0400 @@ -0,0 +1,2 @@ +FILE SCHEME ST arcC aroE glpF gmk pta tpi yqiL +MRSA0252_trimmed.fna saureus 36 2 2 2 2 3 3 2 diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_mrsa_novel.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_mrsa_novel.fasta Mon Oct 15 07:41:48 2018 -0400 @@ -0,0 +1,2 @@ +>saureus.yqiL~2 MRSA0252_trimmed_novel.fna +GCGTTTAAAGACGTGCCAGCCTATGATTTAGGTGCGACTTTAATAGAACATAAAATTAAAGAGACGGGTTTGAATCCAAGTGAGATTAATGAAGTCATCATCGGTAACGTACTACAAGCAGGACAAGGACAAAATCCAGCACGAATTGCTGCTATGAAAGGTGGCTTGCCAGAAACAGTACCTGCATTTACAGTGAATAAAGTATGTGGTTCTGGGTTAAAGTCGATTCAATTAGCATATCAATCTATTGTGACTGGTGAAAATGACATCGTGCTAGCTGGCGGTATGGAGAATATGTCTCAATCACCAATGCTTGTCAACAACAGTCGCTTTGGTTTTAAAATGGGACATCAATCAATGGTTGATAGCATGGTATATGATGGTTTAACAGATGTATTTAATCAATATCATATGGGTATTACTGCTGAAAATTTAGTAGAGCAATATGGTATTTCAAGAGAAGAACAAGATACATTTGCTGTAAACTCACAACAAAAAGCAGTACGTGCACAGCAA diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_mrsa_novel.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_mrsa_novel.txt Mon Oct 15 07:41:48 2018 -0400 @@ -0,0 +1,1 @@ +MRSA0252_trimmed_novel.fna saureus - arcC(-) aroE(-) glpF(-) gmk(-) pta(-) tpi(-) yqiL(~2) diff -r 253b7a1cf87e -r 68cdb40ff91c test-data/output_noresults.txt --- a/test-data/output_noresults.txt Mon Feb 12 05:18:20 2018 -0500 +++ b/test-data/output_noresults.txt Mon Oct 15 07:41:48 2018 -0400 @@ -1,1 +1,1 @@ - - - +Acetobacter.fna - -