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Changeset 0:a3b5bee8ae1b (2019-05-03)

Next changeset 1:093352878303 (2019-05-03)

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diff -r 000000000000 -r a3b5bee8ae1b chewBBACA.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chewBBACA.pl Fri May 03 10:06:09 2019 -0400

[

@@ -0,0 +1,149 @@
+#!/usr/bin/env perl
+## A wrapper script to call chewBBACA.py and collect its output
+use strict;
+use warnings;
+use Cwd;
+use English;
+use File::Copy;
+use File::Basename;
+
+# Parse arguments
+my ($myFunction,
+    $input1,
+    $input1_names,
+    $output,
+    $python) = @ARGV;
+
+# Run program
+my $abs_path = Cwd::abs_path($PROGRAM_NAME);
+my $scriptdir = dirname($abs_path);
+
+prepareEnvironment($input1,$input1_names,"input_dir");
+runChewBBACA();
+collectOutput();
+exit(0);
+
+# Run chewBBACA
+sub runChewBBACA {
+    my $abs_path = Cwd::abs_path($PROGRAM_NAME);
+    my $scriptdir = dirname($abs_path);
+    my $createschemadir = "$scriptdir/createschema";
+    my $allelecalldir = "$scriptdir/allelecall";
+    my $SchemaEvaluatordir = "$scriptdir/SchemaEvaluator";
+    my $utilsdir = "$scriptdir/utils";
+    my $newpath = "PATH=$ENV{PATH}:$createschemadir:$allelecalldir:$SchemaEvaluatordir:$utilsdir";
+    my $result = system("$newpath; $python");
+    return 0;
+}
+
+# Run prepareEnvironment, create the directory $indir with symlinks to the files listed in $inlist
+sub prepareEnvironment {
+    my ($inlist, $inlist_names, $indir) = @_;
+    if ($inlist ne "NULL") {
+      mkdir($indir);
+      my @inputs = split(',', $inlist);
+      if ($inlist_names ne "NULL") {
+        my @inputs_names = split(',', $inlist_names);
+        for my $i ( 0 .. $#inputs ){
+          my $name = $inputs_names[$i];
+          $name =~ s/ /_/g;
+          $name =~ s/\//_/g;
+          $name =~ s/$/_/g;
+          $name =~ s/$/_/g;
+          $name =~ s/\[/_/g;
+          $name =~ s/\]/_/g;
+          $name =~ s/\{/_/g;
+          $name =~ s/\}/_/g;
+          symlink($inputs[$i], $indir . "/" . $name);
+        }
+      }
+      else {
+        foreach my $i (@inputs){
+          symlink($i, $indir . "/" . basename($i));
+        }
+      }
+    }
+    return 0;
+}
+
+# Collect output
+sub collectOutput{
+    # CreateSchema
+    if ($myFunction eq "CreateSchema") {
+      my($dataname, $datadir, $datasuffix) = fileparse($output,qr/\.[^.]*/);
+      my @fasta_files = glob "output_dir/*.fasta";
+      my $dest_dir = $datadir . $dataname . "/";
+      mkdir($dest_dir);
+      open(my $fh1, '>', $output) or die "Could not open file '$output' $!";
+      my $new_fasta_file = "";
+      foreach my $fasta_file (@fasta_files) {
+         $new_fasta_file = $dest_dir . basename($fasta_file);
+         print $fh1 "$new_fasta_file\n";
+         move($fasta_file, $new_fasta_file) or die "Could not move $fasta_file: $!\n";
+      }
+      close $fh1;
+      my @short_fasta_files = glob "output_dir/short/*.fasta";
+      my $short_dest_dir = $datadir . $dataname . "/short/";
+      mkdir($short_dest_dir);
+      foreach my $short_fasta_file (@short_fasta_files) {
+         move($short_fasta_file, $short_dest_dir) or die "Could not move $short_fasta_file: $!\n";
+      }
+    }
+    # AlleleCall
+    if ($myFunction eq "AlleleCall") {
+      my @outputs = split(',', $output);
+      my @statistics = glob "output_dir/results_*/results_statistics.tsv";
+      if (@statistics == 1) {
+        move($statistics[0], $outputs[0])
+      }
+      my @contigsinfo = glob "output_dir/results_*/results_contigsInfo.tsv";
+      if (@contigsinfo == 1) {
+        move($contigsinfo[0], $outputs[1])
+      }
+      my @alleles = glob "output_dir/results_*/results_alleles.tsv";
+      if (@alleles == 1) {
+        move($alleles[0], $outputs[2])
+      }
+      my @logginginfo = glob "output_dir/results_*/logging_info.txt";
+      if (@logginginfo == 1) {
+        move($logginginfo[0], $outputs[3])
+      }
+      my @repeatedloci = glob "output_dir/results_*/RepeatedLoci.txt";
+      if (@repeatedloci == 1) {
+        move($repeatedloci[0], $outputs[4])
+      }
+    }
+    # SchemaEvaluator
+    if ($myFunction eq "SchemaEvaluator") {
+      my($dataname, $datadir, $datasuffix) = fileparse($output,qr/\.[^.]*/);
+      my @output_files = glob "output_rms/*.*";
+      my $dest_dir = $dataname . "/";
+      mkdir($dest_dir);
+      my $new_output_file = "";
+      foreach my $output_file (@output_files) {
+         $new_output_file = $dest_dir . basename($output_file);
+         move($output_file, $new_output_file) or die "Could not move $output_file: $!\n";
+      }
+      open(my $fh2, '<', $dest_dir . "SchemaEvaluator.html") || die "File not found";
+      my @lines = <$fh2>;
+      close($fh2);
+      my @newlines;
+      foreach(@lines) {
+         $_ =~ s/\.\.\/\.\.\/\.\.\/.*?\/database\/files\/...\/dataset/dataset/g;
+         push(@newlines,$_);
+      }
+      # write the html to the Galaxy output file
+      #open($fh2, '>', $output) || die "File not found";
+      #print $fh2 @newlines;
+      #close($fh2);
+      my @html_output_files = glob "output_rms/genes_html/*.*";
+      my $html_dest_dir = $dest_dir . "genes_html/";
+      mkdir($html_dest_dir);
+      foreach my $html_output_file (@html_output_files) {
+         move($html_output_file, $html_dest_dir) or die "Could not move $html_output_file: $!\n";
+      }
+      my $cmd = `tar -cpf $output $dest_dir`;
+    }
+    return 0;
+}
+

diff -r 000000000000 -r a3b5bee8ae1b chewbbaca.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chewbbaca.xml Fri May 03 10:06:09 2019 -0400

[

b'@@ -0,0 +1,305 @@\n+<tool id="chewBBACA" name="chewBBACA" version="2.0">\n+ <description>BSR-Based Allele Calling Algorithm\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="3.6">Python</requirement>\n+ <requirement type="package" version="1.15.3">numpy</requirement>\n+ <requirement type="package" version="0.19.1">scipy</requirement>\n+ <requirement type="package" version="5.22.2.1">perl</requirement>\n+ <requirement type="package" version="1.72">biopython</requirement>\n+ <requirement type="package" version="3.8.1">plotly</requirement>\n+ <requirement type="package" version="1.8.2">SPARQLWrapper</requirement>\n+ <requirement type="package" version="0.23.4">pandas</requirement>\n+ <requirement type="package" version="2.5.0">blast</requirement>\n+ <requirement type="package" version="2.6.3">prodigal</requirement>\n+ <requirement type="package" version="2.1">clustalw</requirement>\n+ <requirement type="package" version="7.313">mafft</requirement>\n+ <requirement type="package" version="2.0.16">chewbbaca</requirement>\n+ </requirements>\n+ \n+ <stdio>\n+ \n+ <exit_code range="1:" level="fatal" description="Tool exception" />\n+ <exit_code range=":-1" level="fatal" description="Tool exception" />\n+ </stdio>\n+ <command>\n+ perl \n+ $__tool_directory__/chewBBACA.pl $selectFunction.myFunctions\n+ #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\')\n+ \'${",".join(map(str, $selectFunction.input1))}\'\n+ #elif str( $selectFunction.myFunctions ) in (\'SchemaEvaluator\', \'TestGenomeQuality\', \'ExtractCgMLST\', \'RemoveGenes\')\n+ $selectFunction.input1\n+ #else\n+ \'NULL\'\n+ #end if\n+ #if str( $selectFunction.myFunctions ) == \'AlleleCall\'\n+ #set $input_names = []\n+ #for $input in $selectFunction.input1\n+ $input_names.append($input.element_identifier)\n+ #end for\n+ #set $input_name = ",".join(map(str, $input_names))\n+ \'$input_name\'\n+ #else\n+ \'NULL\'\n+ #end if\n+ #if str( $selectFunction.myFunctions ) == \'CreateSchema\'\n+ \'$schema\'\n+ #elif str( $selectFunction.myFunctions ) == \'AlleleCall\'\n+ \'$statistics,$contigsinfo,$alleles,$logginginfo,$repeatedloci\'\n+ #elif str( $selectFunction.myFunctions ) == \'SchemaEvaluator\'\n+ \'$schemaplot\'\n+ #elif str( $selectFunction.myFunctions ) == \'TestGenomeQuality\'\n+ \'$thresholdplot,$removedgenomes\'\n+ #elif str( $selectFunction.myFunctions ) == \'RemoveGenes\'\n+ \'$removedgenes\'\n+ #else\n+ \'NULL\'\n+ #end if\n+\n+ "chewBBACA.py $selectFunction.myFunctions\n+ #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\', \'TestGenomeQuality\', \'ExtractCgMLST\')\n+ -o output_dir\n+ #end if\n+ #if str( $selectFunction.myFunctions ) == \'RemoveGenes\'\n+ -o output_removegenes\n+ #end if\n+ #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\')\n+ -i input_dir\n+ --cpu \\${GALAXY_SLOTS:-4}\n+ #end if\n+ #if str( $selectFunction.myFunctions ) in (\'SchemaEvaluator\', \'TestGenomeQuality\', \'ExtractCgMLST\', \'RemoveGenes\')\n+ -i $selectFunction.input1\n+ #end if\n+ #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\')\n+ #if $selectFunction.bsr\n+ --bsr $selectFunction.bsr\n+ #end if\n+\n+ #if $selectFunction.ptfmode.ptf_select=="system"\n+ --ptf ${ filter( lambda x: str( x[0] ) == str( $selectFunction.ptfmode.ptf_system ), $__app__.tool_data_tables[ \'chewbb'..b'ctions\'] == "SchemaEvaluator"</filter>\n+ </data>\n+ <data format="html" name="thresholdplot" from_work_dir="output_dir/GenomeQualityPlot.html" label="${tool.name}:TestGenomeQuality on ${on_string}: Plot" >\n+ <filter>selectFunction[\'myFunctions\'] == "TestGenomeQuality"</filter>\n+ </data>\n+ <data format="tsv" name="removedgenomes" from_work_dir="output_dir/removedGenomes.txt" label="${tool.name}:TestGenomeQuality on ${on_string}: Removed genomes" >\n+ <filter>selectFunction[\'myFunctions\'] == "TestGenomeQuality"</filter>\n+ </data>\n+ <data format="tsv" name="cgmlst" from_work_dir="output_dir/cgMLST.tsv" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLST" >\n+ <filter>selectFunction[\'myFunctions\'] == "ExtractCgMLST"</filter>\n+ </data>\n+ <data format="txt" name="cgmlstschema" from_work_dir="output_dir/cgMLSTschema.txt" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLSTschema" >\n+ <filter>selectFunction[\'myFunctions\'] == "ExtractCgMLST"</filter>\n+ </data>\n+ <data format="tsv" name="removedgenes" from_work_dir="output_removegenes.tsv" label="${tool.name}:RemoveGenes on ${on_string}" >\n+ <filter>selectFunction[\'myFunctions\'] == "RemoveGenes"</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="selectFunction[\'myFunctions\']" value="AlleleCall" />\n+ <param name="input1" value="a_contigs.fasta" ftype="fasta" />\n+ <param name="selectFunction.mode[\'schema_select\']" value="system" />\n+ <param name="selectFunction.mode[\'reference\']" value="schema_pubMLST" />\n+ <param name="selectFunction.mode[\'ptf_select\']" value="noptf" />\n+ <output name="statistics" >\n+ <assert_contents>\n+ <has_text text="a_contigs.fasta" />\n+ </assert_contents>\n+\t\t\t</output>\n+ </test>\n+ </tests>\n+ <help>\n+**chewBBACA** stands for "BSR-Based Allele Calling Algorithm". The "chew" part could be thought of as "Comprehensive and Highly Efficient Workflow" \n+but at this point still it needs a bit of work to make that claim so we just add "chew" to add extra coolness to the software name.\n+This tool is in beta test.\n+\n+The development of the tools have been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2\n+("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - \xe2\x80\x9cFundos Europeus Estruturais e de Investimento\xe2\x80\x9d \n+from \xe2\x80\x9cPrograma Operacional Regional Lisboa 2020\xe2\x80\x9d and by national funds from FCT - \xe2\x80\x9cFunda\xc3\xa7\xc3\xa3o para a Ci\xc3\xaancia e a Tecnologia\xe2\x80\x9d and BacGenTrack (TUBITAK/0004/2014) \n+[FCT/ Scientific and Technological Research Council of Turkey (T\xc3\xbcrkiye Bilimsel ve Teknolojik Ara\xc5\x9frrma Kurumu, T\xc3\x9cBITAK)].\n+ </help>\n+ <citations>\n+ <citation type="bibtex">@ARTICLE{andrews_s,\n+ author = {Rossi, M and Silva, M and Ribeiro-Gon\xc3\xa7alves, B and Silva, DN and Machado, MP and Oleastro, M and Borges, V and Isidro, J and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK and Halkilahti,\n+ J and Jaakkonen, A and Palma, F and Culebro, A and Kivist\xc3\xb6, R and H\xc3\xa4nninen, ML and Laukkanen-Ninios, R and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M and Garaizer, J and Bikandi, J and Hilbert,\n+ F and Taboada, EN and Carri\xc3\xa7o, JA},\n+ keywords = {bioinformatics, ngs, mlst},\n+ title = {{INNUENDO whole and core genome MLST databases and schemas for foodborne pathogens}},\n+ url = {https://github.com/TheInnuendoProject/chewBBACA_schemas}\n+ }</citation>\n+ <citation type="doi">10.1099/mgen.0.000166</citation>\n+ <citation type="doi">10.1371/journal.pgen.1007261</citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r a3b5bee8ae1b chewbbaca_ptfs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chewbbaca_ptfs.loc.sample Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+#Prodigal Training Files
+Escherichia_coli Escherichia coli ${__HERE__}/TrainingFiles4Prodigal/trained_eColi.trn
\ No newline at end of file

diff -r 000000000000 -r a3b5bee8ae1b chewbbaca_schemas.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chewbbaca_schemas.loc.sample Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+#schemas
+schema_pubMLST schema_pubMLST ${__HERE__}/schema_ecoli_pubMLST_Achtman/_schema.txt
\ No newline at end of file

diff -r 000000000000 -r a3b5bee8ae1b test-data/TrainingFiles4Prodigal/Escherichia_coli.trn

Binary file test-data/TrainingFiles4Prodigal/Escherichia_coli.trn has changed

diff -r 000000000000 -r a3b5bee8ae1b test-data/a_contigs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a_contigs.fasta Fri May 03 10:06:09 2019 -0400

b'@@ -0,0 +1,97794 @@\n+>NODE_1_length_55894_cov_10.726949\n+GTCACCATTACTGGCGACATGACACCGTTCACCCAATGTACAAACGCGTACTCGCATTCC\n+GGTATTCGCAATCCGACTACTATCTCCAGCGCTGCTTATCCGCGAAGAATTACCGGTTAC\n+AGCAACCCGTGCGCGTTCACCGGAGCTGCCAATGTGACTGTTAAAGCCGACACTTCCAAT\n+CCGCACGCTATAACCCATACTGGCAATTTGCGCGGCATACCCAGCGGTTGCGATTCGGGC\n+GTATCCTCACAACAGCCGATGCGAGCATGATCGTCGCTGCGGGCAAACTGACTGCAAAAT\n+GGTATCTCTCCGGGGTCTGTGGCCAGTTTTTGCATAGAGGAAACTTCCTGATGCGCGAAG\n+TTTTCATCCGCCAGCCATTTTTTCCACGCATACTCAACCAGACTCTCCGCCCAGTCCGTA\n+TATCCTTCCTCAATCAGTGCATGATGAATATCGGCATAACTACCGCCGCGTGGGAAATGG\n+CGCAGGAACCAGCGATACATCACCGCTCCGATACGCCATTCTCGCAGGTCTGCTCGTGTA\n+ATGATCATTCGTTAGTGCCGGTGATAGCCATCGACCATGCTTTTAAAGGTTTCGTGTGGC\n+GTACGCCCCGTGGTGCAAAGATAAAGATGACCGAAGATAAAAAAGAGGCTTATAAATGCC\n+AGAGCAAAATGCGCCTGCAATAACCAGTATCTTACGCCAGGAAACACATCTCCCACGGCT\n+TGCGGATAGAGACACAGCAGCCCCGTCAATAGTAACAACGGCAGCAATCCATACATAACA\n+CCAACATAGGCGACCTGCTGTAAGGGATTAAATTTAGACTGGGTTGTTGCCGGGAAAGGA\n+TGTTCTTCCCCCTGCATAATGCCAAACAAATAAAATCGCGTTTGTTTTGCCGCTCGCTCC\n+AGCCACCCCTGACGACGAATGCGATAGTGGTGACCATTACCCCCAACGGCATTGATCAGC\n+ACAAAGCCGAGCCAGCATGCGAGTAACAAAAATCCGCAAACTTCATGCACCGCAACCAGA\n+CTTTTAACCGCAGTTGCGCCCACCAGCGCAAAGTGATTTATCAGCCCACTTGCCAGCAAC\n+AATACAAAGAGTAACGCATTCGACCAGTGCCATAATCTGACCGCTTTGCAGTAAAGATAA\n+ATCTTCTCACCATAATCGGTGACTGATTTCTTCACGCCACGAGCACGAAGCAAGGCATGC\n+AGCCCCAGCACCAACCACATCCCAACCAGCAATACTCCGGCAATGATCAACCACACCGGC\n+CAAAATTCGGGAGTGAACTGTGGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAGCA\n+TGTTGCGACGGGTTCATACATTTTCCTTTTTAATCAAATGTTGACCGAACCGGCGATACA\n+GATGCGGTTTCCCGGCACCAGGTAGCTGATATTGATAGTATTTATTTTGCTGCAACCACG\n+CCTGAATTTCTGGGCTATCTTCGCGACCAAAGATCAATGCGTGTTCCGGGCAGGCGCTGA\n+CGCAAATGGGCGGAAAGCCTTTTGCCAGTCGGGACTCAGCGCAGAAATCACATTTATCTG\n+CCACTTTAGTGACAGGGTTAAGGTAGCGAACCTGGTACGGACAAGCGCCAATGCAATAAC\n+TGCAGCCGATGCACTGCGATTTTTCTACCCGCACGATCCCCTGCTCATCACGCCACGACG\n+CCCCTGTCGGGCATACGTCGATGCACGGAGCATCTTCGCAGTGCTGACATGACTGGCGAA\n+AAAAGTGATACTGCGTTTCGTTGTCGTTATCGGTGACTGGAATGTGTGCTATCGATAAAC\n+GGCTTCCCTGAGCGGGGACGTGGTTAGTTTTACGGCATGCGCGGGCGCAAATATTACAGC\n+CATTGCACCGTGACTCGTCATGAATCATGGCATACCGAACTTCCTTTTCTTGCCTCGTGT\n+TCGCTAACAGAGAAGACGCAGAACCAGTAAAAAAGATTACTGTTCCCATCCCCAGAACAA\n+ATTTGCGTCGAGTGAAGGACATCTGATTATCCCCTAATGCAGTGGCTGCAACTGTCCACC\n+CTATCCATGACATCTCCCTGAAATTTCAGGGGTTCTGAAACTGCTCTACCTCGAACCATT\n+CGCATAAGCCATAAGCCTTGCCATAGGTCATAAATCGCTCGCTAAACAAGTACAACACCG\n+CCGTCGATGACTCCACCTGCCGTATATCGGCATATTCAGGTGCAACATCCATCGCGGCGA\n+TCGCGGCTTCAATCTGCGCTTCCTGGAAGTAATATGGCGCTTGCATCAGCATGGCGACTT\n+TGTAAGGACGAGGATATGTCTGGCACTCAAAACGAACGGCGTGTGCAATGGCGCGACAAA\n+TGTCCTGCTCCACAACTTGCAAAGACATCGCCGCGTAGTTTTCACTCATGGCCTGCGTTG\n+AGTAATAGTAATCATCCTGGCTTCCCGTCATACAAGCGATATCCGCGTAGTCTCCGTTCT\n+GCTTAATGCTTTCCAGCAAAACTGACAGCTCCTCTTCTGCAACCGAATAGGGTGGCGAGA\n+GAAACACGCGCGCGCCACCAGCTGCCCAGCCGCAGAATGCTGGCGAATGAACTCTGCCAG\n+GATTTCAGCCGGTTCTGGTTCGGTTACCGTATCAACGGGGTGACGCATCCCCTGTAACCA\n+TTGCCGCTTCGCCTCGTCAACTTCGCTGACTTTCGCTAACGGCAATTCATCCCGATGGTT\n+CATCTCACCCATTCCTTACACAGGCAGTAGATTGTGTGCTGCCAGATCGGCGGCAATATC\n+TTCCAGCCCCAGACGCTGCAATGTTTCGCGGGTCGGACAACCAAGCTGTGGGTCCCAGCC\n+CATTTCTTTGTAGAACATCGTGAGCGAAGCATGCATATCGTCACGATCCATTTTGTCAGT\n+ACCTTCAGTAAAGACCGGGATCTGCGGATCCTTGTCGAATACCCAGGAACAGATAAGATC\n+GTGTTCATTACGCATATCTTTGGTTTGCATCAGTTTTACCGTGTAGGCACGATGCAACGT\n+AAAGATACGCTCTGCAGCTAAATCTAATTTTTCCTGAGTCATCTCTTCGCCGGTGATCGC\n+TTTGAAGAATTTGGCTTCAAGCGCCAGATCGCCCCGGTAATTACGGCTTTTCAGCGGCGA\n+AACGGTCATTGGCCAGACCCAGTTGCACAGGGTGACGGCGTTATGCAAACAGACCCGCAA\n+CAGCGACCACTTTGCATATTTAATTTTTGCGTCATTGATTGGCGTGTAGTTTTTGGTTTC\n+ATCGTAGGCATCTTCAGAACCAAAAAGCTCTTTCGCCACTTCACGCTGCAGTTTCAATGG\n+CAAACCCGAACCAATAAAATTGATATGGGTATGCGTCATGCAGTCACGGTTGAACATACA\n+GTTAACAATGGAACCGACCTGCGCTGACGCTTCATTGGCATGGTGAACCGGATAGCCAAA\n+CGGCGACCAGAGTTTATTTTTTGCGTAGCCCCAGTACTCTTCACCCAAATTCCAGCGTTC\n+TGCGATGGCATATGAACCATCAGCCAGGTGACTCAGCTCACCCACACGATGCGCCAGACG\n+GTAGTAAAAATCTTTAATGAAATTAACGTCACCCGCTTCCAGTTGATCCCAGTGAATTTC\n+CGCATACTCTTCAGCTGGCAGAACACGCTTGAACACCCCTTTGCTGTAACAATAAGTAAA\n+GTCGCGATGCAGCTGCCCGTAGTTACACCATAGGCCGTAGTCATCGAACAAATTCAGACC\n+AACCAGGTTACCAATCACACGACCATCGTCTTTATCTTCAAAATCTTTCGGCCCGTTCGG\n+GAAGATGGTGGTATGGACAAAGTTAGCTACACAAGT'..b'53_length_87_cov_6.437500\n+AAGTCACGTTCAGTGTGGCCTGACCGTTATAACCTTCAGCGCTGCTGCCGCTGACACTGT\n+GGGCATAACCGGCCTGAACGCCCAGGG\n+>NODE_2754_length_85_cov_18.166667\n+GTTTATCGAACTCATCCGCCACAGCCCCGCCCGTGTAACCACACTCATCAGAGCGGTAGG\n+TCCACATACAGGTATTCGCCAGCAT\n+>NODE_2755_length_83_cov_50.571429\n+CTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGT\n+GCTGAAGCAACAAATGCCCTGCT\n+>NODE_2756_length_82_cov_33.851852\n+ACCACCTGCGTGATTACCCTGTCCTGCTCCGGGATAATGCCATTCTAATCTGACTCCAGA\n+ATGTCTGCCGGTCCCAGCCCAG\n+>NODE_2757_length_82_cov_7.259259\n+GTGAATATGTACCCGGACAGCGGACAGCGGACAGCGGACAGTGCCATCCGTTCGGACGCA\n+GTGTGATGCGCTGGGAGACGGG\n+>NODE_2758_length_81_cov_19.076923\n+TAAGCTGCTGCAGATGATGCGGGTTCTCATCACTCAGCAGGTTGCCCCATTCATCATATT\n+CTGCGCACCACGCTGTTGCCC\n+>NODE_2759_length_77_cov_26.272727\n+ACAGAGGCGTGATGACAATATGGTCTTTCCGATGGCTCATAAAGAAAATTAACCTGATTA\n+CGAGGGTCATCCTCTTT\n+>NODE_2760_length_76_cov_49.333333\n+ATATGGTGATTTTGAAAATGGTATTCCTGTTCACGATACTATTGCCAGAGTTGTATCCTG\n+TATCAGTCCTGCAAAA\n+>NODE_2761_length_76_cov_37.952381\n+GTGGTGATGAAGAAATCCACAGCAGGCATCAGTATCAGCTGAATTTTATAACCCATATAC\n+GGGCGCCAGAAATGGC\n+>NODE_2762_length_72_cov_26.823529\n+GGGGTTATTCCTTCCCCGTTGAGGACACCGGGTTGTCAGGTTGACCATACGCTTAAGTGA\n+CAACCCCGCTGC\n+>NODE_2763_length_72_cov_25.294118\n+TCACCGTCATCTGCTGGCCGCCGAACTGCTCCGCATCCACCTGCAGCCCCACAATGGCCG\n+TGTTCGGGTAGC\n+>NODE_2764_length_72_cov_22.176471\n+TCACCGTCATCTGCTGACCGCCGAACTGCTCCGCATCCACCTGCAGCCCCACAATGGCCG\n+TGTTCGGGTAGC\n+>NODE_2765_length_71_cov_43.312500\n+ACAGATGGCGCACTCATCACCGGACTGACCTTTCTTGACCCCAAAGATGCCACACGGGTT\n+CAGGGTTTTTT\n+>NODE_2766_length_71_cov_20.750000\n+ACCCAGTGGTTGGTCATCGCACCGCGACCAAATGTTGGAGCAAGACTTGCTACCGTTGGT\n+CCGTGTCAGAC\n+>NODE_2767_length_70_cov_22.400000\n+AAAACAGAGAAAGGAAACGACAGAGGCCAAAAAGCTCGTTTTCAGCACCTGTCGTTTCCT\n+TTCTTTTCAG\n+>NODE_2768_length_65_cov_7.000000\n+TCCAGTCGGTGCACCAATCCCGTGGCCATCAGATACCGTTCCGTCTGGCTATGCCTGATG\n+CAGGG\n+>NODE_2769_length_63_cov_53.250000\n+AAAGTTTCATCCATTTTCTCCACCCAGGTTGCGGAAGAACCACTTTTGCACCGTTCGTGA\n+CAG\n+>NODE_2770_length_63_cov_40.125000\n+ATCCAGCCCCTTAACATCCTGCCACGGCCCGTCACCAAACCTGACCTGCAAATGCTGAAA\n+AAA\n+>NODE_2771_length_63_cov_30.875000\n+TTGACGGCACCTGGATGATGCGACCGCGGATATGGTAGTTCACCGTCATCTGCTGGCCGC\n+CGA\n+>NODE_2772_length_63_cov_26.000000\n+AAGTCGCCACTTTTTTTAAAGAGGCATCCCTTAAAACCTTGCCATCAAAAGTCGCCACTT\n+TTT\n+>NODE_2773_length_62_cov_113.428571\n+ATGTTAAGGGGCTGGATGAAGTGGGCAGTGATACAGGCAGAACAGGAGAATGACATGAAT\n+AT\n+>NODE_2774_length_60_cov_39.800000\n+TCCCCGGTTGAGAATCTTCATACACGGTGATGGTCCCGGCATGTGACGGCGGGAATCCTT\n+>NODE_2775_length_60_cov_30.600000\n+TACCGGGTTGAGAATCTTCATACACGGTGATGGTCCCGGCATGTGACGGCGGGAATCCTT\n+>NODE_2776_length_60_cov_18.800000\n+GCAGTCTGAAACCGGCATACAGCAACAACCCGGCCTGGTGCCTGTGGGACATGCTGACTC\n+>NODE_2777_length_60_cov_18.000000\n+TCCCCGGTTGAGAATCTTCATACACGGTGATGGTCCCGGCATGTGACGGCGGGAAGCCCT\n+>NODE_2778_length_59_cov_11.250000\n+CCAACTGGATATGCATTTTTCCGGGCTGATGTACGCTGTACTCAGCCTGTTTTTTTGCG\n+>NODE_2779_length_59_cov_9.500000\n+GCTGAGCGCACGCGGAACAGTTAAAACCAAAAACAGTGTTATGGGTGGATTCTCTGTAT\n+>NODE_2780_length_59_cov_7.500000\n+TCGCAAAAAACAGGCTGAGTACAGCGTACATCAGCCCGGAAAAATGCATATCCAGTTGG\n+>NODE_2781_length_58_cov_38.333333\n+GACAGTAAGCGACTCGTCAGAACCGTATTGATATTTACTGAGAGCTCAGATCAACTTT\n+>NODE_2782_length_58_cov_36.000000\n+AGCGCACGCGGAACAGTTAAAACCAAAAACAGTGTTATGGGTGGATTCTCTGTATCCG\n+>NODE_2783_length_58_cov_29.666667\n+TTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTTTCGG\n+>NODE_2784_length_58_cov_24.666667\n+AAAAAGGCAAGAAGCCCGGTTTCCCCGGGGACCCAAAAAAGGGCCGTTTTTCCCGCCC\n+>NODE_2785_length_58_cov_13.666667\n+CTATCCAGTCGCAGTTCCCCCAGGCACTGCGGGCTTCCTGAAAGCTGAAGCGCGCTTT\n+>NODE_2786_length_58_cov_8.333333\n+TAAACCTTGGTTTAAGAGAACTCGGTACCAGCGGTGAAAAGATCCCCCTGTTGAGCAC\n+>NODE_2787_length_57_cov_43.500000\n+TAATGGTGCGCGTCACCGGCTTTGCCTTCGTCACTTCCACGCCCAGTGCGGTTTCAG\n+>NODE_2788_length_57_cov_35.000000\n+ACCACGGTGGTGGTGAACACGGTGGCCTCTGAAAATCCGGATGAAGCCGGTCGTTAC\n+>NODE_2789_length_56_cov_85.000000\n+GCGATTGTTGCCAGACAGGACAATTTTCACAAGACGTCGCAGATGGGGCGCTTACG\n+>NODE_2790_length_56_cov_13.000000\n+CCGTCAGAAGCAGAGCGCAGCACTGACGGATCTGATGGATCAGTACGTGCTCCTGT\n'

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/_schema.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/_schema.txt Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,9 @@
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/purA-protein1.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/mdh-protein4.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/mdh-protein3.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/icd-protein2.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/gyrB-protein26.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/fumC-protein9.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/fumC-protein3.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/fumC-protein13.fasta
+/home/biolinu/mytools/chewbbaca-galaxy/test-data/schema_ecoli_pubMLST_Achtman/adk-protein33.fasta

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/adk-protein33.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/adk-protein33.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>adk-protein33_1
+ATGGTATTCAACCAGACGTTTACGTACGGTCTCTTCCTGATCGTCTTTACGGATAGTCAGCTCTTCACCGGTAACGTCGTCTTTGCCTTCTACTTTCGGCGGATTGAATTTAACGTGATAAACACGACCAGACGGCGCGTGAACGCGGCGGCCTACGATACGGTCAACAATCAGTTCGTCCGGTACGTCGAATTCCAGAACGTAATCAACATTGATGCCCGCTTCTTTCATCGCGTCTGCCTGCGGAATGGTACGCGGGAAGCCGTCCAACAGGAAACCGTTGCGGCAGTCTTCCTGAGCAATGCGCTCTTTAACCAGCGCGATCACCAGTTCGTCGGTGACCAGTTTGCCAGCATCCATAATGTCTTTTGCTTGTTTACCCAGCTCGGAGCCTGA

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/fumC-protein13.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/fumC-protein13.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>fumC-protein13_1
+ATGTTTGAGATTATGCTCGAGCATCGCTACCCAGCCGGAAATCTCCTGCCCCAGGGTCAGCGGCGTGGCGTCCTGCAAGTGGGTTCGACCGATTTTGACGATATCGGCAAATGCACGCGATTTTTCACTCAGCGTCTGTGTCAGGGTTTTAAGCTGCGGAATGAGTTGCTTGCGCAGCGCCAGCAGCGCCGCAACGTGCATCGCCGTCGGAAAGACATCGTTGGAACTTTGGCTTTTGTTCACGTCGTCGTTAGGGTGAACTTTACGTTCCATCCCGCGCACGCCGCCGAGTAA

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/fumC-protein3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/fumC-protein3.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>fumC-protein3_1
+ATGCTTAAGATTGTGCTCCAGCATTGCCACCCAGCCGGAGATCTCCTGACCAAGCGTCAGCGGCGTGGCGTCCTGAAGGTGCGTACGACCAATTTTAACGATGTCGCGGAAGGCCTGCGCTTTCTCGTTAAGCGTAGATTTAAGCACGTTGAGCTGCGGGATAAGCTGCTCGCGGATTGCGATGACGGCCGCCACGTGCATGGCCGTCGGGAACACGTCGTTGGAACTCTGGCTTTTGTTCACGTCATCGTTCGGGTGGACCTTGCGCTCCATGCCGCGCACGCCGCCAAGAAGCTCGCTTGCGCGGTTCGCCAGCACCTCGTTCATGTTCATGTTGCTCTGGGTGCCTGA

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/fumC-protein9.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/fumC-protein9.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>fumC-protein9_1
+ATGAACGAAGTGCTGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGCGGGATGGAACGTAAAGTTCACCCTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACGTTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACGCAGACACTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGCAGGACGCCACGCCGCTAACACTAGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCTAG

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/gyrB-protein26.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/gyrB-protein26.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>gyrB-protein26_1
+GTGGATCGGCGTTTTGTTCTTGTTCAGATATTCAACGAACGCCTTGATGCCACCTTCATAGTGGAAGTGGTCTTCTTTGCCGTCGCGCTTGTCGCGCAGACGAATGGAAACGCCGGAGTTGAGGAACGACAACTCACGCAGACGTTTCGCCAGAATTTCATATTCGAACTCGGTCACATTGGTGAAGGTTTCGAGGCTGGGCCAGAAACGCACCATGGTGCCGGTTTTTTCAGTCTCGCCGGTAACCGCCAGCGGGGCCTGCGGTACACCGTGTTCGTAGATCTGACGGTGAATTTTACCCTCGCGCTGGATAACCAGCTCCAGTTTTTGCGACAGGGCGTTTACTACCGAAACACCAACGCCGTGTAG

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/icd-protein2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/icd-protein2.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>icd-protein2_1
+ATGGAAATTTACACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGGTGAAGAAAATTCGCTTCCCGGAACATTGTGGTATCGGTATTAA

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/mdh-protein3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/mdh-protein3.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>mdh-protein3_1
+ATGACCGCCGATAACCGGCACTTCCACTTCCGTTGGCTGCTTGCCTTTCAGCTCAGCCACGAAGGTATTGGAGCGGATGATATCCAGCGTAGTTACGCCGAACAGTTTGTTCTTGTCGTAAACGCCCGCTTTCTTCAGCACTTCTGCTGCAATAGCAACGGTGGTGTTCACCGGGTTGGTGATGATCCCGATGCACGCTTTCGGGCAGGTTTCAGCAATCTGCTGAACCAGGTTTTTCACGATGCCCGCGTTGACGTTGAACAGGTCTGA

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/mdh-protein4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/mdh-protein4.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>mdh-protein4_1
+ATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATCGTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATCACTAACCCGGTTAACACCACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTTTATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACTTTTGTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCACTCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCTAG

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/purA-protein1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/purA-protein1.fasta Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,2 @@
+>purA-protein1_1
+GTGGTCGATATCCAGCAGCGTACCCTGCGCACCTTCAAACATGACGAAATCGCCACGCTGACGCGCCTGGTCGAGCAGGTCAGAAACGTCAACAACCATAGAAGTCAGGATGTCGGCAACAGCCATCGTATCATCCAGAACTTTCTGGTAATCAACCGCTTCAGCTTTGTAGTAGTTAACCAACTGGAAGTTGTGATATTCCATCACTTCTTTCAGTTTTTCAGCGAAGGTTTCTTTGTCGAAAAGGTCGCCAACACGTAG

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/adk-protein33_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/adk-protein33_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/adk-protein33_short.fasta_bsr.txt

Binary file test-data/schema_ecoli_pubMLST_Achtman/short/adk-protein33_short.fasta_bsr.txt has changed

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein13_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein13_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein13_short.fasta_bsr.txt

Binary file test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein13_short.fasta_bsr.txt has changed

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein3_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein3_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein3_short.fasta_bsr.txt

Binary file test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein3_short.fasta_bsr.txt has changed

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein9_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein9_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein9_short.fasta_bsr.txt

Binary file test-data/schema_ecoli_pubMLST_Achtman/short/fumC-protein9_short.fasta_bsr.txt has changed

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/gyrB-protein26_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/gyrB-protein26_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/gyrB-protein26_short.fasta_bsr.txt

Binary file test-data/schema_ecoli_pubMLST_Achtman/short/gyrB-protein26_short.fasta_bsr.txt has changed

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/icd-protein2_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/icd-protein2_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/icd-protein2_short.fasta_bsr.txt

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diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/mdh-protein3_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/mdh-protein3_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/mdh-protein3_short.fasta_bsr.txt

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diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/mdh-protein4_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/mdh-protein4_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/mdh-protein4_short.fasta_bsr.txt

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diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/purA-protein1_short.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_ecoli_pubMLST_Achtman/short/purA-protein1_short.fasta Fri May 03 10:06:09 2019 -0400

diff -r 000000000000 -r a3b5bee8ae1b test-data/schema_ecoli_pubMLST_Achtman/short/purA-protein1_short.fasta_bsr.txt

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diff -r 000000000000 -r a3b5bee8ae1b tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri May 03 10:06:09 2019 -0400

@@ -0,0 +1,10 @@
+<tables>
+    <table name="chewbbaca_schemas" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/chewbbaca_schemas.loc.sample" />
+    </table>
+    <table name="chewbbaca_ptfs" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/chewbbaca_ptfs.loc.sample" />
+    </table>
+</tables>
\ No newline at end of file