| Next changeset 1:269da71211ff (2017-09-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44 |
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added:
megahit_wrapper.xml test-data/paired-fq1.fa test-data/paired-fq2.fa test-data/paired_result.fa test-data/refExample.fa test-data/single_result.fa |
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| diff -r 000000000000 -r 02a822e32de7 megahit_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/megahit_wrapper.xml Sun Sep 24 10:40:12 2017 -0400 |
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| @@ -0,0 +1,117 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool id="megahit" name="MEGAHIT" version="1.1.2"> + <description>metagenomics assembly</description> + <requirements> + <requirement type="package" version="1.1.2">megahit</requirement> + </requirements> + <version_command>megahit --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + + megahit + + #if $input_option.choice == 'paired' + -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.fastq_input1]) } + -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) } + #else + -r '${input_option.single_files}' + #end if + + ##basic assembly + --min-count '${basic_section.min_count}' + --k-min '${basic_section.k_min}' + --k-max '${basic_section.k_max}' + --k-step '${basic_section.k_step}' + --min-contig-len '${basic_section.min_contig_len}' + + ##advanced assembly + ${advanced_section.nomercy} + --bubble-level '${advanced_section.bubble_level}' + --merge-level '${advanced_section.merge_level}' + --prune-level '${advanced_section.prune_level}' + --low-local-ratio '${advanced_section.low_local_ratio}' + ${advanced_section.nolocal} + ${advanced_section.kmin1pass} + + && + + cat megahit_out/log + + ]]></command> + + <inputs> + <conditional name="input_option"> + <param name="choice" type="select" label="Select your input option"> + <option value="single" selected="true">Single</option> + <option value="paired">Paired-end</option> + </param> + <when value="paired"> + <param name="fastq_input1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="list:paired" label="Select a paired collection"/> + </when> + <when value="single"> + <param name="single_files" multiple="true" format="fastq,fastqsanger,fasta" type="data" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" /> + </when> + </conditional> + <section name="basic_section" title="Basic assembly options" expanded="True"> + <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" /> + <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/> + <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="127" help="must be odd number"/> + <param name="k_max" argument="--k-max" type="integer" value="99" label="maximum kmer size" max="127" help="must be odd number"/> + <param name="k_step" argument="--k-step" type="integer" value="20" label="increment of kmer size of each iteration" max="28" help="must be even number"/> + </section> + <section name="advanced_section" title="Advanced assembly options" expanded="False"> + <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue="" label="do not add mercy kmers" /> + <param name="bubble_level" argument="--bubble-level" type="integer" value="0" min="0" max="2" label="intensity of bubble merging (0-2), 0 to disable" /> + <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles" value="20,0.98" /> + <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="2" label="strength of local low depth pruning" /> + <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" /> + <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" /> + <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" /> + </section> + </inputs> + <outputs> + <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <conditional name="input_option"> + <param name="choice" value="single"/> + <param name="single_files" value="refExample.fa" ftype="fasta"/> + </conditional> + <output name="output" file="single_result.fa"/> + </test> + <test> + <conditional name="input_option"> + <param name="choice" value="paired"/> + <param name="fastq_input1"> + <collection type="list:paired"> + <element name="Pair1"> + <collection type="paired"> + <element name="forward" value="paired-fq1.fa" ftype="fasta"/> + <element name="reverse" value="paired-fq2.fa" ftype="fasta"/> + </collection> + </element> + </collection> + </param> + </conditional> + <output name="output" file="paired_result.fa"/> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + +MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. + +-------- + +**Project links:** + +https://github.com/voutcn/megahit + + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btv033</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 02a822e32de7 test-data/paired-fq1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired-fq1.fa Sun Sep 24 10:40:12 2017 -0400 |
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@@\n+>M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n+>M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n+>M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n+>M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n+>M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n+>M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n+>M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n+>M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACACA\n+>M01368:8:000000000-A3GHV:1:1102:13809:1733/1\n+ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGAGGGCTATTTAGGTTTTATGCTGTCTCTTATACACATCTCCG\n+>M01368:8:000000000-A3GHV:1:1102:17584:10050/1\n+ATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCT\n+>M01368:8:000000000-A3GHV:1:1102:18842:24844/1\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCT\n+>M01368:8:000000000-A3GHV:1:1102:21788:11027/1\n+GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTG\n+>M01368:8:000000000-A3GHV:1:1102:5728:8777/1\n+ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG\n+>M01368:8:000000000-A3GHV:1:1102:5983:21093/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGT'..b'CCATGCATTTGGTATTTTCGTCTGGGCGGTGTCCACGCAATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA\n+>M01368:8:000000000-A3GHV:1:1112:10272:7828/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTT\n+>M01368:8:000000000-A3GHV:1:1112:9832:16531/1\n+CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGCTGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTTGAAGTAGGAACC\n+>M01368:8:000000000-A3GHV:1:1112:9832:6701/1\n+CGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGA\n+>M01368:8:000000000-A3GHV:1:1113:13532:8618/1\n+GGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGCTACAGTTCACTTTAGCTACCTCCAAGTGTTATG\n+>M01368:8:000000000-A3GHV:1:1113:21679:18011/1\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGAGGGTGTGCACGCGATAGCATTGCGAGACGCTTGAGCCGGAGCACCCTATGTCGCAGTATATGTCTTTGATTCCTGCCTCTTCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACTGTCTCTTATACACATATCCACGCCCACGAGACTAAGGCGAAGTTCATT\n+>M01368:8:000000000-A3GHV:1:1113:25528:14016/1\n+CCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGG\n+>M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA\n+>M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA\n+>M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n+>M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA\n+>M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n+>M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n+>M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA\n' 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| diff -r 000000000000 -r 02a822e32de7 test-data/paired-fq2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired-fq2.fa Sun Sep 24 10:40:12 2017 -0400 |
| b |
| b'@@ -0,0 +1,200 @@\n+>M01368:8:000000000-A3GHV:1:1101:6911:8255/2\n+TCGCCTTACCGCTACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG\n+>M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n+>M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n+>M01368:8:000000000-A3GHV:1:1101:25545:21098/2\n+GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\n+>M01368:8:000000000-A3GHV:1:1101:5446:12248/2\n+ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT\n+>M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n+>M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCCA\n+>M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGCTGTCTCTTATACACA\n+>M01368:8:000000000-A3GHV:1:1102:13809:1733/2\n+NATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATCTGTCTCTTATACACATCTGAC\n+>M01368:8:000000000-A3GHV:1:1102:17584:10050/2\n+GTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGATCTTGGGGGGTGG\n+>M01368:8:000000000-A3GHV:1:1102:18842:24844/2\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n+>M01368:8:000000000-A3GHV:1:1102:21788:11027/2\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCCTG\n+>M01368:8:000000000-A3GHV:1:1102:5728:8777/2\n+CACTTGGGAGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC\n+>M01368:8:000000000-A3GHV:1:1102:5983:21093/2\n+ATTGAACGTAGGTGCGATAAATAATAGGAT'..b'TGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATG\n+>M01368:8:000000000-A3GHV:1:1112:10272:7828/2\n+GTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG\n+>M01368:8:000000000-A3GHV:1:1112:9832:16531/2\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n+>M01368:8:000000000-A3GHV:1:1112:9832:6701/2\n+GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATT\n+>M01368:8:000000000-A3GHV:1:1113:13532:8618/2\n+GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTGGAT\n+>M01368:8:000000000-A3GHV:1:1113:21679:18011/2\n+TTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCTGTCTCTTATACACATCTGACGCTGCCGACGACCGAGCTAGTTGAGATC\n+>M01368:8:000000000-A3GHV:1:1113:25528:14016/2\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n+>M01368:8:000000000-A3GHV:1:1113:5741:16959/2\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n+>M01368:8:000000000-A3GHV:1:1114:10130:11959/2\n+ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGAGTTCTGTGGGGCCGGGGATCCTTATAAAAAAAATAGA\n+>M01368:8:000000000-A3GHV:1:1114:14540:5315/2\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC\n+>M01368:8:000000000-A3GHV:1:1114:15066:16302/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG\n+>M01368:8:000000000-A3GHV:1:1114:16639:15258/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG\n+>M01368:8:000000000-A3GHV:1:1114:2404:13066/2\n+ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACATT\n+>M01368:8:000000000-A3GHV:1:1114:9184:6959/2\n+AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTTA\n' |
| b |
| diff -r 000000000000 -r 02a822e32de7 test-data/paired_result.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_result.fa Sun Sep 24 10:40:12 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>k99_1 flag=1 multi=111.0000 len=390 +CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG |
| b |
| diff -r 000000000000 -r 02a822e32de7 test-data/refExample.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refExample.fa Sun Sep 24 10:40:12 2017 -0400 |
| b |
| @@ -0,0 +1,19 @@ +>megahit_ref_example +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC +TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA +TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC +ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG +CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA +GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC +AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG +AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT +GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT +GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT +TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT +GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG +GCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTG +CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC +TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT +CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG +CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC |
| b |
| diff -r 000000000000 -r 02a822e32de7 test-data/single_result.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/single_result.fa Sun Sep 24 10:40:12 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>k21_1 flag=3 multi=1.0486 len=576 +GGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAAC |