remove capitalization and hyphens

tools/seqTK-nml/seqTK-nml.pl

-#!/usr/bin/env perl
-
-use strict;
-use Bio::SeqIO;
-
-my ($fastaref, $type, $coverage, $outfile, $outfile_rev, $length, $subsample_size, @fastqs, $rv);
-
-$fastaref = $ARGV[0];
-shift(@ARGV);
-$type = $ARGV[0];
-shift(@ARGV);
-if ($type eq "single"){
-	$fastqs[0] = $ARGV[0];
-	shift(@ARGV);
-}else{
-	$fastqs[0] = $ARGV[0];
-	shift(@ARGV);
-	$fastqs[1] = $ARGV[0];
-	shift(@ARGV);	
-}
-$coverage = $ARGV[0];
-shift(@ARGV);
-$outfile = $ARGV[0];
-shift(@ARGV);
-if ($type ne "single"){
-	$outfile_rev = $ARGV[0];
-	shift(@ARGV);
-}
-	
-if (!($coverage)){
-	$coverage = 50;
-}
-
-my $seq_in  = Bio::SeqIO->new(
-  -format => 'fasta',
-  -file   => $fastaref,
-);
-
-while ( my $seq = $seq_in->next_seq()) {
-    $length += $seq->length();
-}
-
-my $all_fastq = join (' ' , map { "\"$_\"" } @fastqs);
-
-#one liner from : http://onetipperday.blogspot.ca/2012/05/simple-way-to-get-reads-length.html with some modification by Philip Mabon
-my $total=`cat $all_fastq | perl -ne '\$s=<>;<>;<>;chomp(\$s);print length(\$s)."\n";' | sort | uniq -c | perl -e 'while(my \$line=<>){chomp \$line; \$line =~s/^\\s+//;(\$l,\$n)=split/\\s+/,\$line; \$t+= \$l*\$n;} print "\$t\n"'`;
-
-print "Total number of Basepairs: $total\n";
-print "Length of Reference: $length\n";
-
-my $rawcoverage = $total/$length;
-printf "Raw Coverage: %.3f\n",$rawcoverage;
-
-my $out = $outfile;
-my $i = 0;
-if($rawcoverage > $coverage){
-	#need to downsample
-	#calculate $subsample_size
-	$subsample_size = $coverage/$rawcoverage;
-	printf("subsample: %.3f",$subsample_size);
-	#printf()
-	my $out = $outfile;
-	my $i = 0;
-	foreach my $fastq (@fastqs){
-		if($i > 0){
-			$out = $outfile_rev;
-		}
-		#seed always set to 42 for reproducibility 
-		my $seqCommand = "seqtk sample -s42 $fastq $subsample_size > $out";
-		$rv = system($seqCommand);
-		$i ++;
-	}	
-} else {
-	#no sampling needed, just copy the fastq's to the output
-	print "Subsampling not required\n";
-	foreach my $fastq (@fastqs){
-		if($i > 0){
-			$out = $outfile_rev;
-		}
-		my $copyCommand = "scp $fastq $out";
-		$rv = system($copyCommand);
-		$i ++;
-	}
-}
-
-
-exit $rv >> 8 if $rv >>8;
-
-#return $rv >> 8;

tools/seqTK-nml/seqTK-nml.xml

-<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="0.0.1">
-	<description>Runs seqTK sample if raw coverage is above user defined threshold </description>
-	<requirements>
-		<requirement type="package" version="1.0-r75-dirty">seqtk</requirement>
-		<requirement type="package" version="5.18.1">perl</requirement>
-		<requirement type="package" version="1.6.922">bioperl</requirement>
-	</requirements>
-	<command interpreter="perl">
-		seqTK-nml.pl $fastar 
-
-		#if $single_or_paired.type == "single"
-			single
- 			$input_se
- 			$coverage $output
-		#elif $single_or_paired.type == "paired"
-            paired
-          	$single_or_paired.forward_pe $single_or_paired.reverse_pe
-          	$coverage $output $output_rev
-        #else
-            collection
-            $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse
-            $coverage $output_collection.forward $output_collection.reverse
-        #end if
-
-	</command>
-	<stdio>
-		<exit_code range="1:" level="fatal" description="Unknown error has occured"/>
-	</stdio>
-	<inputs>
-		<conditional name="single_or_paired">
-			<param name="type" type="select" label="Read type">
-				<option value="single">Single-end</option>
-                <option value="paired">Paired-end</option>
-                <option value="collection">Collection Paired-end</option>
-			</param>
-			<when value="single">
-				<param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
-			</when>
-			<when value="paired">
-				<param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
-                <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
-            </when>
-            <when value="collection">
-                <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
-            </when>
-        </conditional>
-        
-		<param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
-		<param name="coverage" type="integer" label="Desired Coverage" value="50" />
-	</inputs>
-
-	<outputs>
-		
-		<data format="fastqsanger" name="output" label="SubSampled Fastq" >
-			<filter>single_or_paired['type']!="collection"</filter>
-		</data>
-		<data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
-			<filter>single_or_paired['type']=="paired"</filter>
-		</data>
-		<collection name="output_collection" type="paired" label="SubSampled Fastqs">
-			<data name="forward" format="fastqsanger"/>
-      		<data name="reverse" format="fastqsanger"/>
-			<filter>single_or_paired['type']=="collection"</filter>
-		</collection>
-	</outputs>
-
-	<tests>
-		<test>
-			<param name="type" value="paired" />
-			<param name="forward_pe" value="inputforward.fastq" />
-			<param name="reverse_pe" value="inputreverse.fastq" />
-			<param name="fastar" value="testref.fasta"/>
-			<param name="coverage" value="50" />
-			<output name="output" file="outputforward.fastq" />
-			<output name="output_rev" file="outputreverse.fastq" />
-		</test>
-
-	</tests>
-	<help>
-What it does
-============
-
-Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads. 
-
-
-Usage
-=====
-
-**Parameters**
-	- Fastq reads (single end, paired end, or paired end collection)
-	- Fasta reference file
-
-**Options**
-	- Desired coverage (50)
-	</help>
-</tool>
-

tools/seqTK-nml/test-data/testref.fasta

->gi|360034408|ref|NC_016445.1|_2000000_2400000
-CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT
-CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA
-TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG
-TCGTGCGCCGTCTGTAAACCCAATTCAAGCCAAATTTCATAACCTTGCTGCACATAATCGGCGAGCAACTTAAGCACCGC
-ATCCGGTACACAATCAGGACGAGTGCCAACACACAACCCCACAATATCCGCTTCTTCTAGGGCTTGTTCGTACATGGATT
-TCAGCACTTGCACTTCCGCATACGTGCTGGTGTAAGCTTGAAAATAAGCGAGGTATTTTTTGGCGCGTTTGATCTCCCCC
-GCCCGATCTTTCAACTGCGCTTGAATACTCTGCTGCTGAGTATTTTCATCGGCAAACGACGCCACATTACAGAAAGTGCA
-GCCGCCACGGCCTATCGTGCCATCGCGATTCGGACAACTGAATCCACCATGCAGCGTTAACTTATGGACCTTCTCTCCAT
-AACGGCGTTGTAAATCTTGACCTATGGTGTTCACCAGTTGATGTAAATGCATCGGCTCGCTCAATCTAAATACAAATATC
-TCTCACTACCATCCGTGTAATTTAATTACATTTCCAATCGAATTGGTCACAAATTTTAATCCCTCGCGTTTGATTTCAAA
-CAGCGTCAAATCAATAAATAGGCATAAAATAAACACTATTTGCATTTTGTTTCTAGTTTGTTAAACAAAACATTCATCTA
-GCTGTAAAAAAATAAACCAAACCGCAGACTTTTCGTTGGAATTTGCGCCAGCAAAATTGTAGGATACTTTCAGTTTTCCG
-TGCTTTTTTGCTCAATTAATTACAAAAAACGCGGCAGACTATCGGTGATATTCCACACCTACCAAAAGAATCCACTAGTA
-AAGTGGCTCGACAACAGGAATGTCACTAAGGATTGTCTTTCTCACAATATATTTCCTGTGAGAGACGGAAAGGACGCGGA
-TCTGCTCCCTAAGCAGATTTCACTCAAAACAAAAAGGACAGGACGTATCGCCCAAGCGACTCATTCAGCGGATGCTGCTT
-GATGCGTGGCGGGAATAACTGAGTGCACACTCAGTGCGGTTGCGTCCTCAATAACTGGAAGGATGTATCTATGGTAGATA
-AAGCGCAACGTTCGCGTGGTCTTTATACGCCTGAGCTGGAGCATGATGCTTGTGGCATCGGCTTTGTCGCTCACCTGAAA
-AATCGCAAGTCTCATCAGGTGGTCACTCAAGCTTTGGACATGCTCGCACGCATGGAACACCGTGGCGGTCAGGGTTGTGA
-CCCTTGCAGCGGTGACGGTGCGGGTATTTTGTTGCAAAAACCTCACGAATTTTTACTCGAAGAAGCGGTTAAACTGGGGA
-TCAAGCTGCCTTCATTCGAAAAGTACGGTGTTGGTGTGGTGCTGTTCCCGAAAGATGAACATAAACGCGCCCAATGCCGC
-GACATTCTAGAACGCAATGCCAAACGCCTTGATCTGGATGTGATTGGCTACCGCGTTTTACCGACCAATAACAGCATGTT
-GGGTGCCGACCCCCTCAGTACCGAACCACAATTTGAACACGTGTTTATTTCTGGCGGCCCGGGTATGCAGCCTGACGAGC
-TAGAACGCAAGCTGTACGTGCTGCGTAACTACACCGTTCGCGTCTGCCTTGAGAGCGTGTCGAACATCGGTGATGATTTT
-TATATCAACTCGATGTCGTACAAAACCTTGGTCTATAAAGGTCAGTTGACTACAGAGCAAGTACCGCAATACTTCCTCGA
-CTTGCAAAATCCGACCATGGTGACAGCGTTAGCACTGGTGCACTCGCGTTTTTCGACCAACACCTTCCCGAAATGGCGAC
-TGGCTCAACCTTTCCGCTACATCGCGCACAACGGTGAGATCAACACGGTTCGCGGTAACTTGAACTGGATGAAAGCGCGC
-GAAGCGATTTTACAATCCAAGCTGTTTACTCAAGCTGAAATCGATATGCTGCTGCCTATCTGCCAAGAAGGCGCATCCGA
-TTCGGCTAACTTTGACATGGTACTCGAACTGCTGGTGCTTTCCGGTCGCAGCTTGCCTCACGCTCTGATGATGATGATCC
-CAGAAGCATGGCAAGAAAACAAAGCGATGGATCCTAAGCGCCGCGCCTTCTATCAATACCACGCTAACGTCATGGAACCT
-TGGGACGGCCCAGCATCAGTGTGCTTTACCGATGGGGTACAAGTAGGCGCCACACTGGATCGTAACGGTCTGCGTCCGTC
-TCGTTATACCGTGACCAAAGACGATTTTCTGATCATGGCTTCCGAATCTGGCGTCGTGGAAATTGATCCGGCCAATGTGG
-AATACCGTGGTCGTCTGCAACCGGGACGTATCTTTGTTGCCGACTTAGAACAAGGCCGTATTATCTCAGATGAAGAGGTG
-AAAGACGGTATCGCTTCGGCGCAGCCTTATGAAAAATGGGTAGAAGAAAACCTACTCAGTTTGAAAAAACTGCCGGATGC
-CGACAACGTACATAGCCAACCGTCGCCAGAGCGTCTCCTCCATCGCCAACAAGCGTTTGGGGTGAGTAGCGAAGAGGTCA
-ATGACATCATTCTGACTCTCGCGCAAACTGGTTATGAGCCGCTCGGTTCGATGGGGGCAGACTGGCCGGTCGCCGTGCTG
-TCACACCAATCTCAGCATCTCTCCAACTACTTCAAGCAGTTGTTTGCCCAAGTGACCAACCCACCGATCGACCCGATCCG
-TGAACGCATGGTGATGTCGCTCAACACTTATATCGGCCGCGATCAAAACTTGCTAGCAGAAACCCCTGCGCACTGTCGTA
-AGGTCGAATTGGAATCGCCGGTCATTTCTAATGCTGAGCTTGAGAAAATCCGGGCAATCGATAACGAGCACTTGCAAGCC
-AAAACCTTAGACATCGTATTTCGTGCCAGCGATGAACCGGGCAAGCTCGAACGCGCTCTGAAACGTATTTGCCAATACGC
-GGAAGATGCGGTGATTGATGGCTATTCGATCATTTTGCTGACCGACCGCGCGGTAAACTCCAACCACGCCGCCATCCCAG
-CCATGCTGGCTGTAGGCGCGGTGCACCATCACCTGATCCGCAAAGGTCTGCGTTCGAAATGCGGCATTGTGGTGGAAACT
-GGTGATGCGCGTGAAACGCACCACTTTGCAACCCTACTCGGCTACGGTGCAAACGCAGTCAACCCGTATCTAGTGGTGGA
-AACCATCGTCGATCTCAAGCGTCAGAAGAAACTCGATGCCGATGTTTCGGTAGAGAAATACTTCGAGAATTACCGTAAAG
-GCGTGAACGGCGGTCTGTTGAAGATCTTCTCTAAAATGGGGATTTCGACGCTGCAGTCTTATCACGGTGCACAGATTTTT
-GAAGCGCTCGGGATCAGTAAAGCGGTGGTCGATAAATACTTCACTGGCACCATCACCCGTATTCAAGGTTTGACCCTCGA
-CGACATCGCTAAAGAAGTGTTGGTTCGTCATCGCATTGGTTACCCAACGCGTGAAATCCCACTGCAAGTGCTGGATGTCG
-GCGGCGTGTATCAATGGAAACAGCGTGGTGAGCAGCATCTGTTTAACCCAGAAACGATTCACCTGCTGCAAGAATCGACT
-CGCCACAAAAATTATCAGCAGTTCAAGAAGTACGCAGCCGCGGTGGATAGCCAAGGCGATAAAGCCGTTACTCTGCGCAG
-TCAGCTTGATTTTGTGAAAAATCCAGCGGGTTCCATTCCGATTGAGGAAGTGGAACCGATCGAGAGCATTGTGAAGCGCT
-TTGCCACCGGTGCGATGTCGTTTGGGTCTATCTCTTACGAAGCGCACTCCACACTGGCGATTGCGATGAACCGTCTAGGC
-GCGAAATCCAACTCCGGTGAAGGTGGTGAAGACCCAATGCGTTTTGAGCTAAATGCCAACGGTGATTCAGAGCGTTCAGC
-GATCAAGCAAGTAGCATCTGGCCGTTTCGGCGTGACCTCTTACTATCTGACCAACGCAGATGAAATCCAGATCAAGATGG
-CGCAAGGGGCGAAACCGGGCGAAGGTGGTCAGCTACCGGGTGATAAAGTCGATGAATGGATCGGGGCAACTCGTCACTCG
-ACACCGGGCGTCGGCCTGATTTCGCCACCACCGCACCACGACATTTACTCTATCGAAGACTTAGCCCAGCTGATTTTCGA
-TCTGAAAAACGCCAACCGCAAAGGTCGCGTCAACGTCAAACTGGTTTCTGAAGCCGGTGTCGGCACCATCGCATCGGGTG
-TGGCTAAAGCCAAAGCTGACGTAGTACTGATTGCCGGTCACGATGGCGGTACGGGTGCATCACCCATCTCTTCTATCCGT
-CATACCGGTTTACCTTGGGAACTGGGTCTGGCTGAAACCCACCAGACTCTGCTCAAAAACGGCCTGCGTAACCGCATTGT
-GGTGCAAGCCGATGGACAGATGAAAACCCCACGCGATATCGCGATTGCGGTACTGTTGGGCGCTGAAGAATGGGGCGTCG
-CAACCGCTGCACTGGTGGTTGAAGGCTGTATCATGATGCGTAAATGTCATAAAAACACTTGCCCTGTCGGTATCGCCACA
-CAAAACAAAACTCTGCGTGAGCGTTTTGCTGGCCGTGTGGATGACGTTGTGACCTTCTTCCAATACATGGCACAAGGCCT
-GCGTGAAATCATGGCTGAGCTCGGTTTCCGCACCATTAACGAAATGGTTGGCCAAGCGCACAAACTCAAAGTGCGTGATG
-ATATTGGCCACTGGAAGTACAAAAACCTCGATCTGTCGCCGATCCTCTTTATTGAGCAGCCGCGCAGCGAAGATGGTATT
-TACTGCCAGACTCAGCAGAACCACCAGCTCGAAAGCATACTGGATCGCACCTTGATCCAATTAGCAACGCCTGCCCTTGA
-GCGTGGTGAAGCGGTCAAAGCAGAGCTACCGATCATCAACACCGATCGCAGTACCGGCACCATGTTGTCTAACGAAATCT
-GTAAGGTTTACAAAGACCAAGGTCTACCACAGCCAATGCAGGTGAAATTCAACGGCAGTGCGGGACAATCTTTCGGGGCA
-TTCCTCACTAAAGGCGTTTACTTTGAAGTGGAAGGCGATGCTAACGACTACTGGGGCAAAGGTCTTTCTGGTGGCACGCT
-GGTGCTCTACCCGAACCGTAACGCCACCATAGTTCCGGAAGAGAACATTGTGGTCGGTAACGTCTGTTTCTACGGCGCAA
-CCTCTGGCGAATCTTACATTCGCGGCCTAGCGGGCGAGCGTTTCTGCGTGCGTAACTCAGGTGCCAAAGTGGTGGTGGAA
-GGTATCGGCGATCACGGCTGTGAATACATGACCGGCGGTGTCGCAGTGATCCTCGGTTCAACCGGCCGTAACTTCGCCGC
-AGGTATGAGTGGCGGTGTGGCTTACGTGTGGGATAAATCTGGCGACTTCCAATCTAAGCTCAATGCAGAATTGGTTGATC
-TGGACCCTATCGAAGCGGAAGACAGAGCCCTACTCAAAGAGATGTTAACCAAGCATGTTCAATTCACAGGAAGTGAAGTG
-GCCAAAGCTTTCCTTGCCAACTTTGACGCAAGCCTAGCCACTATGGTCAAGGTCATGCCGCGTGATTACAAAGCGGTACT
-GCAAAAGCGTAAAGCACAGGAGCAACAAGCCACATTAGCAGCGGAGGCGGTATAAATGGGTAAAGCAACCGGATTTTTAG
-AATTTGGTCGTGAACTGCCGAAAAAAATCGACCCGGCAGAGCGCATCAAAAACAACAAAGAGTTTGTCCTTAACCAAGAG
-TTTGGTAAGAAGATCAATCAGCAAGCTTCACGTTGTATGGATTGTGGCGTGCCGTTTTGTCATAACGGCTGCCCGATTGG
-CAACATCATTCCCGAGTTTAACGATGCAGTGTATCGCGACAGTTGGGAAGAGGCTTGGAATATTCTGAGCTCGACCAACA
-ACTTCCCAGAGTTTACCGGTCGTGTCTGCCCTGCACCTTGTGAAACCGCCTGTGTGCTTGGCATCAACCAAGATCCGATC
-ACCATCTGTAACATTGAAAAAACCATTGTGGAACGTGCTTACCAAGAAGGCTATGCCAAGCCGAAAACGCCACGTTCACG
-CACCGGAAAAACGGTCGCGATCATTGGCTCAGGCCCTGCGGGGCTGGCCGCGGCGGAGCAGTTGAATGCCGCGGGTCATA
-GCGTCACCGTGTTTGAGCGGGATGAAAAAGTCGGCGGCTTGCTGCGCTTTGGCATTCCCGATTTCAAACTCGGTATGGAT
-GTGATTGATCGCAAAATCAATCTGATGGAACAAGCGGGCGTTAAGTTCGTGGTCAATGCGCATATCGGTGTAGACATCAA
-CGCTCAACAGTTGCGTCAGGAGTTTGATGCGGTATTGCTGACGGGCGGCTCAACCGTACCACGTGATCTGAGCATTCCCG
-GACGTGATCTGAAAGGCGTTTACTTCGCGATGCAGTTCCTCGCGCAAAATAACCGCCGAGCCAATGGCATGGATCTGAAA
-GGTGAAGAGATCCACGCTAAAGGCAAACATGTGGTAGTGATCGGAGGCGGCGATACTGGCTCCGACTGTGTCGGCACCTC
-TAACCGCCACGGCGCTGCGAGTATCACTCAAGTGGAGATCATGCCGATCCCACCGCAAAAGCGCCCAGTGAATATGCCTT
-GGCCGCAATATCCGATGATTCTGCGCACCTCTACCTCTCATGAAGAAGGCTGTGAGCGTCATTGGAACATCCTCACCAAA
-GAGTTCATTGGTAATGAACAAGGTGAAGTGACGGGTCTACGCATCGCTGACATCGTTTGGAAAGATGCAGCCCCCGGTGA
-GCGACCAAGCTTTGACGAAGTGGTGGGCAGTGAACGCGTCATTCCTTGTGATATGGCATTTCTGGCGATGGGCTTCTTGC
-ATCCAGAGCCACACGGCGTGCTTGCTCAGTTGGGGATTAAGCTTGATGAGCGCGGCAATGTGGCGACGCAAGATTTTGCG
-ACCAACCAAAAAGGCGTATTCGCCGCAGGTGATATGCGCACAGGCCAATCCTTGGTGGTGCGCTGTATCAACGAAGGTCG
-CGAATGTGCGCGAGCCGTTGACACCTTCTTGATGGGCAATACCCATCTTGAGGCAAAAGCGGACTCACTCATGCTGTCAG
-CATAATCCTCTGTTGGCGCGGGTGATGCATCCTCATCCGTGTCAACACAACCGTTTCCTTCCATATTGTTTTACTTCGGC
-CAGCACTCCCTGCTGGCCTTTTTTATGCCTATTCTCATCACACGGGATAAAACCTTGAGTTATCTGTAACTGAGAGAAAA
-CTATCCCATTGAATATAATGACATTATTTGAAGTATTCCTCGGCAAATACCCTGCAAACCCTATTTTCAACCAATAACTT
-GACCTTTTGTACAATAAGCTATAGGTTGTGAATTCGGTGAAAATAAAATCCCGCAAAAATGTTAATTAATTAACCTGAAA
-TGTTAGTTAATTATTCAAATTATAAAGATTTAAATGAATAGTTATACCCAAGCTACTTGAAGCCATCGTTAAACGGAAGT
-GGATGAATCCCCATCAGCATAGATAACTATGTGATTGGAGTAGACAGACACCGCCCATACCGAGGCTGTTTCAAGGAGTA
-AGGGAATTGTCATTTACTGTCTGGATGACAGAGATGCAAAGGGAGAATTGCAATGGCTCTATACGATCCAAGTCTTGAAA
-AAGACAACTGTGGATTCGGCTTGATCGCGCACATGGAAGGGCAAGCCAGTCACAAACTCGTTCGTACCGCGATTTCAGCA
-CTTGATCGCATGACTCACCGTGGCGGTATCGCCGCCGATGGTAAAACTGGTGATGGCTGTGGTCTGTTGCTGCAAAAACC
-TGACTCTTATTTGCGCCTGATCGCAGAAGAGCAACATTGGAAACTCAGCAAACAGTACGCGATTGGCATGCTGTTTCTCA
-GCCGAGATCCACACAAAGCGCAGCTGGCACAGCAAATTGTTAACCAAGAACTCGCTAAAGAAACCTTAAGCGTGGCAGGT
-TGGCGCAAAGTGCCCACCAACCCGAAAGTGCTTGGCCCGATAGCCCTCGACTCTTTGCCCGATATTCAACAAGTCTTCAT
-CTCCGCCCCGGCCGGTTGGCGTGAGCGCGATGTTGAGCGCCGTCTGTATATTGCGCGTCGTCGCATTGAAAAACAGATTA
-CGGATGATCGCGATTTCTACATCTGCTCGCTCTCGACTCAAGTGTTGGTTTACAAAGGCCTGTGTATGCCCGCAGACCTA
-CCACGCTTTTATCTCGACTTAGCCGATCTGCGTATGGAATCGGCGATTTGCTTGTTCCACCAACGTTTCTCCACCAATAC
-TCAGCCACGCTGGCCGCTGGCTCAGCCGTTTCGCTATCTGGCGCACAATGGCGAAATCAACACCATTGAAGGTAACCGCC
-AGTGGGCACGCGCTCGGGCTTATAAGTTCGCGTCACCGCTGCTGCCCGATTTGCAAAGCGCTGCCCCTTTTGTGAATGAA
-ACCGGTTCGGACTCTTCGAGCCTAGACAACATGCTGGATCTGTTTTTAGCCGGCGGGATGGATATCTTCCGTGCGATGCG
-CATGCTGGTTCCGCCCGCATGGCAAAACCATCCGGATATGGATCCGGATCTGCGTGCTTTCTACGATTTCAACTCCAAAC
-ACATGGAGCCTTGGGATGGCCCGGCGGGGATCGTGCTGTCCGATGGTCGTTACGCCGCGTGTAACCTTGACCGTAACGGC
-CTGCGTCCTGCGCGTTATGTGATCACCAAAGATAAGCTCATCACCCTCGCTTCAGAAGTCGGGATTTGGGATTACGCACC
-AGATGAAGTGTCTGAAAAAGGTCGGGTTGGCCCCGGCGAGCTGCTGGTGATCGACACTCGCAAAGGCAAAATTTGGCAAT
-CGAGCGAAATTGATAACGACCTAAAAAGCCGTCACCCCTATCGTGAGTGGATGGAAAATAACGTTCATAAACTCACGCCC

tools/seqTK-nml/tool_dependencies.xml

-<?xml version="1.0"?>
-<tool_dependency>
-	<package name="perl" version="5.18.1">
-		<repository name="package_perl_5_18" owner="iuc" />
-	</package>
-    <package name="seqtk" version="1.0-r75-dirty">
-        <repository name="package_seqtk_1_0_r75" owner="iuc"  />
-    </package>
-  	<package name="bioperl" version="1.6.922">
-  		<repository name="package_bioperl_1_6" owner="iuc" />
-    </package>
-</tool_dependency>