| Previous changeset 2:253b7a1cf87e (2018-02-12) Next changeset 4:1f5641a52664 (2018-12-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67 |
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modified:
mlst.xml mlst_list.xml test-data/output_mincov100.txt test-data/output_minid100.txt test-data/output_mrsa.txt test-data/output_noresults.txt |
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added:
macros.xml test-data/MRSA0252_trimmed_novel.fna test-data/output_mrsa_exclude.txt test-data/output_mrsa_legacy.txt test-data/output_mrsa_novel.fasta test-data/output_mrsa_novel.txt |
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| 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 |
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| @@ -0,0 +1,26 @@ +<macros> + <token name="@VERSION@">2.15.1</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.15.1">mlst</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>mlst --version</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{Seemann2016, + author = "Seemann T", + title = "MLST: Scan contig files against PubMLST typing schemes", + year = "2016", + url = {https://github.com/tseemann/mlst} + } + </citation> + </citations> + </xml> +</macros> |
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| 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 |
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| b'@@ -1,28 +1,60 @@\n-<tool id="mlst" name="MLST" version="2.10">\n- <requirements>\n- <requirement type="package" version="2.10">mlst</requirement>\n- </requirements>\n+<tool id="mlst" name="MLST" version="@VERSION@">\n+ <description>Scans genomes against PubMLST schemes.</description>\n+ <macros>\n+ <import>macros.xml</import>\n+\n+ <xml name="legacy_param">\n+ <param argument="--legacy" type="boolean" truevalue="--legacy" falsevalue="" checked="true" label="Include allele header" help="Include allele header row in output table (requires scheme to be set)" />\n+ </xml>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n \n- <version_command>mlst --version</version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+ #import re\n+\n+ ## Creates symlinks for each input file based on the Galaxy \'element_identifier\'\n+ ## Used so that a human-readable name appears in the output table (instead of \'dataset_xyz.dat\')\n+ #set $named_input_files = \'\'\n+ #for $input_file in $input_files\n+ ## Add single quotes around each input file identifier\n+ #set $_input_file = "\'{}\'".format($input_file.element_identifier)\n+ ln -s \'${input_file}\' ${_input_file} &&\n+ #set $named_input_files = $named_input_files + \' \' + $_input_file\n+ #end for\n \n- <command detect_errors="exit_code"><![CDATA[\n- mlst "$input_file" --nopath\n- #if $settings.advanced == "advanced"\n- #if $settings.min_dna_id\n- --minid=$settings.min_dna_id\n+ mlst --nopath\n+ --threads "\\${GALAXY_SLOTS:-1}"\n+ #if str($settings.advanced) == "advanced"\n+ #if str($settings.minid)\n+ --minid=$settings.minid\n+ #end if\n+ #if str($settings.mincov)\n+ --mincov=$settings.mincov\n+ #end if\n+ #if $settings.novel\n+ --novel \'${novel_alleles}\'\n #end if\n- #if $settings.min_dna_cov\n- --mincov=$settings.min_dna_cov\n- #end if\n- #if $settings.scheme\n- --scheme=$settings.scheme\n+ #if str($settings.scheme_condition.set_scheme) == "auto"\n+ #if str($settings.scheme_condition.minscore)\n+ --minscore=$settings.scheme_condition.minscore\n+ #end if\n+ #if str($settings.scheme_condition.exclude)\n+ --exclude \'${settings.scheme_condition.exclude}\'\n+ #end if\n+ #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual"\n+ #if str($settings.scheme_condition.scheme)\n+ --scheme=\'${settings.scheme_condition.scheme}\'\n+ #end if\n+ $settings.scheme_condition.legacy\n #end if\n #end if\n+ ${named_input_files}\n > "$report"\n ]]></command>\n \n <inputs>\n- <param type="data" name="input_file" format="fasta,genbank" />\n+ <param type="data" name="input_files" format="fasta,genbank" multiple="true" />\n <conditional name="settings">\n <param name="advanced" type="select" label="Specify advanced parameters">\n <option value="simple" selected="true">No, use program defaults.</option>\n@@ -31,46 +63,242 @@\n <when value="simple">\n </when>\n <when value="advanced">\n- <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" />\n- <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" />\n- '..b'ram name="advanced" value="advanced"/>\n- <param name="min_dna_id" value="100"/>\n- <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>\n+ <param name="set_scheme" value="list"/>\n+ <param name="scheme" value="saureus"/>\n+ <param name="legacy" value="true"/>\n+ <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>\n+ </test>\n+\n+ <!-- Advanced test - exclude scheme -->\n+ <test>\n+ <param name="input_files" value="MRSA0252_trimmed.fna"/>\n+ <param name="advanced" value="advanced"/>\n+ <param name="set_scheme" value="auto"/>\n+ <param name="exclude" value="saureus"/>\n+ <param name="legacy" value="false"/>\n+ <output name="report" ftype="tabular" file="output_mrsa_exclude.txt"/>\n+ </test>\n+\n+ <!-- Advanced test - output novel alleles. -->\n+ <test>\n+ <param name="input_files" value="MRSA0252_trimmed_novel.fna"/>\n+ <param name="advanced" value="advanced"/>\n+ <param name="minid" value="98"/>\n+ <param name="novel" value="true"/>\n+ <param name="set_scheme" value="manual"/>\n+ <param name="scheme" value="saureus"/>\n+ <param name="legacy" value="false"/>\n+ <output name="report" ftype="tabular" file="output_mrsa_novel.txt"/>\n+ <output name="novel_alleles" ftype="fasta" file="output_mrsa_novel.fasta"/>\n </test>\n </tests>\n \n@@ -95,7 +323,7 @@\n \n **Without auto-detection**\n \n-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.\n+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.\n \n ::\n \n@@ -103,30 +331,27 @@\n \tNM003.fa neisseria 11 2 3 4 3 8 4 6\n \n **Missing data**\n+\n 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:\n \n-+--------+---------------------------+\n-| Symbol | Meaning |\n-+========+===========================+\n-| n | Exact intact allele |\n-+--------+---------------------------+\n-| ~n | Novel allele similar to n |\n-+--------+---------------------------+\n-| n,m | Multiple alleles |\n-+--------+---------------------------+\n-| *-* | Allele missing |\n-+--------+---------------------------+\n++--------+---------------------------------------+\n+| Symbol | Meaning |\n++========+=======================================+\n+| n | Exact intact allele |\n++--------+---------------------------------------+\n+| ~n | Novel full length allele similar to n |\n++--------+---------------------------------------+\n+| n? | Partial match to known allele |\n++--------+---------------------------------------+\n+| n,m | Multiple alleles |\n++--------+---------------------------------------+\n+| *-* | Allele missing |\n++--------+---------------------------------------+\n+\n+Setting **Output novel alleles** to true will produce an additional **novel_alleles.fasta** file containing the novel alleles.\n \n Galaxy wrapper maintained by Simon Gladman.\n ]]></help>\n \n- <citations>\n- <citation type="bibtex">\n- @UNPUBLISHED{Seemann2016,\n- author = "Seemann T",\n- title = "MLST: Scan contig files against PubMLST typing schemes",\n- year = "2016",\n- note = "https://github.com/tseemann/mlst"}\n- </citation>\n- </citations>\n+ <expand macro="citations" />\n </tool>\n' |
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| 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 |
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| @@ -1,9 +1,10 @@ -<tool id="mlst_list" name="MLST List" version="2.10"> - <requirements> - <requirement type="package" version="2.10">mlst</requirement> - </requirements> - - <version_command>mlst --version</version_command> +<tool id="mlst_list" name="MLST List" version="@VERSION@"> + <description>Lists available schemes for the MLST tool.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ mlst $list_type > "$report" @@ -47,13 +48,5 @@ ]]></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> + <expand macro="citations" /> </tool> |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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) |
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| 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 |
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| @@ -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) |
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| 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 |
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| @@ -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) |
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| 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 |
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| @@ -0,0 +1,1 @@ +MRSA0252_trimmed.fna - - |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -0,0 +1,2 @@ +>saureus.yqiL~2 MRSA0252_trimmed_novel.fna +GCGTTTAAAGACGTGCCAGCCTATGATTTAGGTGCGACTTTAATAGAACATAAAATTAAAGAGACGGGTTTGAATCCAAGTGAGATTAATGAAGTCATCATCGGTAACGTACTACAAGCAGGACAAGGACAAAATCCAGCACGAATTGCTGCTATGAAAGGTGGCTTGCCAGAAACAGTACCTGCATTTACAGTGAATAAAGTATGTGGTTCTGGGTTAAAGTCGATTCAATTAGCATATCAATCTATTGTGACTGGTGAAAATGACATCGTGCTAGCTGGCGGTATGGAGAATATGTCTCAATCACCAATGCTTGTCAACAACAGTCGCTTTGGTTTTAAAATGGGACATCAATCAATGGTTGATAGCATGGTATATGATGGTTTAACAGATGTATTTAATCAATATCATATGGGTATTACTGCTGAAAATTTAGTAGAGCAATATGGTATTTCAAGAGAAGAACAAGATACATTTGCTGTAAACTCACAACAAAAAGCAGTACGTGCACAGCAA |
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| 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 |
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| @@ -0,0 +1,1 @@ +MRSA0252_trimmed_novel.fna saureus - arcC(-) aroE(-) glpF(-) gmk(-) pta(-) tpi(-) yqiL(~2) |
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| 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 |
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| @@ -1,1 +1,1 @@ - - - +Acetobacter.fna - - |