Mercurial > repos > iuc > mlst
changeset 3:68cdb40ff91c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
| author | iuc |
|---|---|
| date | Mon, 15 Oct 2018 07:41:48 -0400 |
| parents | 253b7a1cf87e |
| children | 1f5641a52664 |
| files | macros.xml mlst.xml mlst_list.xml test-data/MRSA0252_trimmed_novel.fna test-data/output_mincov100.txt test-data/output_minid100.txt test-data/output_mrsa.txt test-data/output_mrsa_exclude.txt test-data/output_mrsa_legacy.txt test-data/output_mrsa_novel.fasta test-data/output_mrsa_novel.txt test-data/output_noresults.txt |
| diffstat | 12 files changed, 338 insertions(+), 70 deletions(-) [+] |
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--- /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 @@ +<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 + @UNPUBLISHED{Seemann2016, + author = "Seemann T", + title = "MLST: Scan contig files against PubMLST typing schemes", + year = "2016", + url =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>
--- 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 @@ -<tool id="mlst" name="MLST" version="2.10"> - <requirements> - <requirement type="package" version="2.10">mlst</requirement> - </requirements> +<tool id="mlst" name="MLST" version="@VERSION@"> + <description>Scans genomes against PubMLST schemes.</description> + <macros> + <import>macros.xml</import> + + <xml name="legacy_param"> + <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)" /> + </xml> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> - <version_command>mlst --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + #import re + + ## Creates symlinks for each input file based on the Galaxy 'element_identifier' + ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') + #set $named_input_files = '' + #for $input_file in $input_files + ## Add single quotes around each input file identifier + #set $_input_file = "'{}'".format($input_file.element_identifier) + ln -s '${input_file}' ${_input_file} && + #set $named_input_files = $named_input_files + ' ' + $_input_file + #end for - <command detect_errors="exit_code"><![CDATA[ - mlst "$input_file" --nopath - #if $settings.advanced == "advanced" - #if $settings.min_dna_id - --minid=$settings.min_dna_id + mlst --nopath + --threads "\${GALAXY_SLOTS:-1}" + #if str($settings.advanced) == "advanced" + #if str($settings.minid) + --minid=$settings.minid + #end if + #if str($settings.mincov) + --mincov=$settings.mincov + #end if + #if $settings.novel + --novel '${novel_alleles}' #end if - #if $settings.min_dna_cov - --mincov=$settings.min_dna_cov - #end if - #if $settings.scheme - --scheme=$settings.scheme + #if str($settings.scheme_condition.set_scheme) == "auto" + #if str($settings.scheme_condition.minscore) + --minscore=$settings.scheme_condition.minscore + #end if + #if str($settings.scheme_condition.exclude) + --exclude '${settings.scheme_condition.exclude}' + #end if + #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual" + #if str($settings.scheme_condition.scheme) + --scheme='${settings.scheme_condition.scheme}' + #end if + $settings.scheme_condition.legacy #end if #end if + ${named_input_files} > "$report" ]]></command> <inputs> - <param type="data" name="input_file" format="fasta,genbank" /> + <param type="data" name="input_files" format="fasta,genbank" multiple="true" /> <conditional name="settings"> <param name="advanced" type="select" label="Specify advanced parameters"> <option value="simple" selected="true">No, use program defaults.</option> @@ -31,46 +63,242 @@ <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" /> + <param argument="--minid" 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 argument="--mincov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" /> + <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" /> + <conditional name="scheme_condition"> + <param name="set_scheme" type="select" label="Automatically set MLST scheme"> + <option value="auto" selected="true">Automatic MLST scheme detection</option> + <option value="list">Select from a list of MLST schemes</option> + <option value="manual">Manually set MLST scheme</option> + </param> + <when value="auto"> + <param argument="--minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" /> + <param argument="--exclude" type="text" area="false" label="Exclude these schemes" help="Ignore these schemes from auto detection (comma sep. list) (default 'ecoli_2,abaumannii')" optional="true" /> + </when> + <when value="list"> + <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme"> + <option value="achromobacter">achromobacter</option> + <option value="vvulnificus">vvulnificus</option> + <option value="cglabrata">cglabrata</option> + <option value="sthermophilus_2">sthermophilus_2</option> + <option value="mmassiliense">mmassiliense</option> + <option value="bhampsonii">bhampsonii</option> + <option value="afumigatus">afumigatus</option> + <option value="ecloacae">ecloacae</option> + <option value="brucella">brucella</option> + <option value="spseudintermedius">spseudintermedius</option> + <option value="kpneumoniae">kpneumoniae</option> + <option value="edwardsiella">edwardsiella</option> + <option value="chlamydiales">chlamydiales</option> + <option value="leptospira_2">leptospira_2</option> + <option value="neisseria">neisseria</option> + <option value="vcholerae">vcholerae</option> + <option value="orhinotracheale">orhinotracheale</option> + <option value="paeruginosa">paeruginosa</option> + <option value="lsalivarius">lsalivarius</option> + <option value="leptospira">leptospira</option> + <option value="sepidermidis">sepidermidis</option> + <option value="mhyorhinis">mhyorhinis</option> + <option value="bcc">bcc</option> + <option value="yruckeri">yruckeri</option> + <option value="suberis">suberis</option> + <option value="yersinia">yersinia</option> + <option value="taylorella">taylorella</option> + <option value="kaerogenes">kaerogenes</option> + <option value="xfastidiosa">xfastidiosa</option> + <option value="bordetella">bordetella</option> + <option value="cbotulinum">cbotulinum</option> + <option value="hpylori">hpylori</option> + <option value="mpneumoniae">mpneumoniae</option> + <option value="sdysgalactiae">sdysgalactiae</option> + <option value="efaecium">efaecium</option> + <option value="aphagocytophilum">aphagocytophilum</option> + <option value="ecoli_2">ecoli_2</option> + <option value="ganatis">ganatis</option> + <option value="mhyopneumoniae">mhyopneumoniae</option> + <option value="bsubtilis">bsubtilis</option> + <option value="tenacibaculum">tenacibaculum</option> + <option value="campylobacter">campylobacter</option> + <option value="ranatipestifer">ranatipestifer</option> + <option value="mcaseolyticus">mcaseolyticus</option> + <option value="csputorum">csputorum</option> + <option value="csinensis">csinensis</option> + <option value="dnodosus">dnodosus</option> + <option value="koxytoca">koxytoca</option> + <option value="soralis">soralis</option> + <option value="bcereus">bcereus</option> + <option value="wolbachia">wolbachia</option> + <option value="saureus">saureus</option> + <option value="hcinaedi">hcinaedi</option> + <option value="clari">clari</option> + <option value="leptospira_3">leptospira_3</option> + <option value="sinorhizobium">sinorhizobium</option> + <option value="pmultocida_multihost">pmultocida_multihost</option> + <option value="ecoli">ecoli</option> + <option value="pdamselae">pdamselae</option> + <option value="pmultocida_rirdc">pmultocida_rirdc</option> + <option value="bhyodysenteriae">bhyodysenteriae</option> + <option value="cupsaliensis">cupsaliensis</option> + <option value="efaecalis">efaecalis</option> + <option value="shaemolyticus">shaemolyticus</option> + <option value="rhodococcus">rhodococcus</option> + <option value="pacnes">pacnes</option> + <option value="szooepidemicus">szooepidemicus</option> + <option value="pgingivalis">pgingivalis</option> + <option value="cfetus">cfetus</option> + <option value="bpilosicoli">bpilosicoli</option> + <option value="kseptempunctata">kseptempunctata</option> + <option value="streptomyces">streptomyces</option> + <option value="smaltophilia">smaltophilia</option> + <option value="ppentosaceus">ppentosaceus</option> + <option value="cronobacter">cronobacter</option> + <option value="mhaemolytica">mhaemolytica</option> + <option value="cdiphtheriae">cdiphtheriae</option> + <option value="vcholerae2">vcholerae2</option> + <option value="chyointestinalis">chyointestinalis</option> + <option value="borrelia">borrelia</option> + <option value="abaumannii">abaumannii</option> + <option value="arcobacter">arcobacter</option> + <option value="csepticum">csepticum</option> + <option value="mcanis">mcanis</option> + <option value="pfluorescens">pfluorescens</option> + <option value="lmonocytogenes">lmonocytogenes</option> + <option value="sgallolyticus">sgallolyticus</option> + <option value="cfreundii">cfreundii</option> + <option value="mplutonius">mplutonius</option> + <option value="vibrio">vibrio</option> + <option value="bbacilliformis">bbacilliformis</option> + <option value="ypseudotuberculosis">ypseudotuberculosis</option> + <option value="vparahaemolyticus">vparahaemolyticus</option> + <option value="mcatarrhalis">mcatarrhalis</option> + <option value="bintermedia">bintermedia</option> + <option value="sagalactiae">sagalactiae</option> + <option value="kkingae">kkingae</option> + <option value="bpseudomallei">bpseudomallei</option> + <option value="bhenselae">bhenselae</option> + <option value="spneumoniae">spneumoniae</option> + <option value="vtapetis">vtapetis</option> + <option value="senterica">senterica</option> + <option value="mabscessus">mabscessus</option> + <option value="sthermophilus">sthermophilus</option> + <option value="brachyspira">brachyspira</option> + <option value="mbovis">mbovis</option> + <option value="hsuis">hsuis</option> + <option value="spyogenes">spyogenes</option> + <option value="cconcisus">cconcisus</option> + <option value="cmaltaromaticum">cmaltaromaticum</option> + <option value="abaumannii_2">abaumannii_2</option> + <option value="aeromonas">aeromonas</option> + <option value="miowae">miowae</option> + <option value="shominis">shominis</option> + <option value="otsutsugamushi">otsutsugamushi</option> + <option value="hinfluenzae">hinfluenzae</option> + <option value="clanienae">clanienae</option> + <option value="sbsec">sbsec</option> + <option value="scanis">scanis</option> + <option value="msynoviae">msynoviae</option> + <option value="hparasuis">hparasuis</option> + <option value="magalactiae">magalactiae</option> + <option value="chelveticus">chelveticus</option> + <option value="fpsychrophilum">fpsychrophilum</option> + <option value="ssuis">ssuis</option> + <option value="cdifficile">cdifficile</option> + <option value="cinsulaenigrae">cinsulaenigrae</option> + <option value="blicheniformis">blicheniformis</option> + <option value="slugdunensis">slugdunensis</option> + <option value="plarvae">plarvae</option> + </param> + <expand macro="legacy_param" /> + </when> + <when value="manual"> + <param name="scheme" type="text" area="false" label="MLST Scheme (manual)" help="Enter a MLST scheme to use (see output of 'MLST List' tool for a list of available schemes)" /> + <expand macro="legacy_param" /> + </when> + </conditional> </when> </conditional> </inputs> <outputs> - <data name="report" format="tabular" /> + <data name="report" format="tabular" label="${tool.name} on ${on_string}: report.tsv"/> + <data name="novel_alleles" format="fasta" label="${tool.name} on ${on_string}: novel_alleles.fasta"> + <filter>settings['advanced'] == "advanced" and settings['novel']</filter> + </data> </outputs> <tests> <!-- Basic test - will produce no results. --> <test> - <param name="input_file" value="Acetobacter.fna"/> + <param name="input_files" value="Acetobacter.fna"/> <param name="advanced" value="simple"/> - <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/> + <output name="report" ftype="tabular" file="output_noresults.txt"/> </test> <!-- Basic test - will produce results. --> <test> - <param name="input_file" value="MRSA0252_trimmed.fna"/> + <param name="input_files" value="MRSA0252_trimmed.fna"/> <param name="advanced" value="simple"/> - <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/> + <output name="report" ftype="tabular" file="output_mrsa.txt"/> </test> <!-- Advanced test - Min DNA Coverage 100 --> <test> - <param name="input_file" value="MRSA0252_trimmed.fna"/> + <param name="input_files" 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"/> + <param name="mincov" value="100"/> + <output name="report" ftype="tabular" file="output_mincov100.txt"/> </test> <!-- Advanced test - Min DNA ID 100 --> <test> - <param name="input_file" value="MRSA0252_trimmed.fna"/> + <param name="input_files" value="MRSA0252_trimmed.fna"/> + <param name="advanced" value="advanced"/> + <param name="minid" value="100"/> + <output name="report" ftype="tabular" file="output_minid100.txt"/> + </test> + + <!-- Advanced test - Manually set MLST scheme --> + <test> + <param name="input_files" value="MRSA0252_trimmed.fna"/> + <param name="advanced" value="advanced"/> + <param name="set_scheme" value="manual"/> + <param name="scheme" value="saureus"/> + <param name="legacy" value="true"/> + <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/> + </test> + + <!-- Advanced test - Set a MLST scheme from a list --> + <test> + <param name="input_files" 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"/> + <param name="set_scheme" value="list"/> + <param name="scheme" value="saureus"/> + <param name="legacy" value="true"/> + <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/> + </test> + + <!-- Advanced test - exclude scheme --> + <test> + <param name="input_files" value="MRSA0252_trimmed.fna"/> + <param name="advanced" value="advanced"/> + <param name="set_scheme" value="auto"/> + <param name="exclude" value="saureus"/> + <param name="legacy" value="false"/> + <output name="report" ftype="tabular" file="output_mrsa_exclude.txt"/> + </test> + + <!-- Advanced test - output novel alleles. --> + <test> + <param name="input_files" value="MRSA0252_trimmed_novel.fna"/> + <param name="advanced" value="advanced"/> + <param name="minid" value="98"/> + <param name="novel" value="true"/> + <param name="set_scheme" value="manual"/> + <param name="scheme" value="saureus"/> + <param name="legacy" value="false"/> + <output name="report" ftype="tabular" file="output_mrsa_novel.txt"/> + <output name="novel_alleles" ftype="fasta" file="output_mrsa_novel.fasta"/> </test> </tests> @@ -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. ]]></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> + <expand macro="citations" /> </tool>
--- 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 @@ -<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>
--- /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
--- 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)
--- 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)
--- 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)
--- /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 - -
--- /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
--- /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