Galaxy |

Changeset 0:e3698ac146d7 (2017-10-03)

Next changeset 1:4deefd708943 (2021-05-06)

Commit message:
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1

added:
bio_hansel.xml
test-data/SRR1002850_SMALL.fasta
test-data/SRR5646583_SMALL_1.fastq
test-data/SRR5646583_SMALL_2.fastq

diff -r 000000000000 -r e3698ac146d7 bio_hansel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bio_hansel.xml Tue Oct 03 10:39:11 2017 -0400

[

b'@@ -0,0 +1,267 @@\n+<tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.0">\n+ <requirements>\n+ <requirement type="package" version="0.1.0">bio_hansel</requirement>\n+ <requirement type="package" version="17.2.0">attrs</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ## Preparing file input.\n+ #if $data_type.type == "paired":\n+\n+ ln -s \'$data_type.fastq_input1\' fast_q_paired_1.fastq &&\n+ ln -s \'$data_type.fastq_input2\' fast_q_paired_2.fastq &&\n+\n+ #elif $data_type.type == "collection":\n+\n+ ln -s \'$data_type.fastq_input1.forward\' fast_q_paired_1.fastq &&\n+ ln -s \'$data_type.fastq_input1.reverse\' fast_q_paired_2.fastq &&\n+\n+ #elif $data_type.type == "single":\n+\n+ #if $data_type.fastq_input1.is_of_type(\'fastqsanger\') or $data_type.fastq_input1.is_of_type(\'fastq\'):\n+ ln -s \'$data_type.fastq_input1\' fast_q_single.fastq &&\n+ #end if\n+\n+ #if $data_type.fastq_input1.is_of_type(\'fasta\'):\n+ ln -s \'$data_type.fastq_input1\' fast_a_single.fasta &&\n+ #end if\n+\n+ #end if\n+\n+\n+ ## Checking for custom scheme.\n+ #if $type_of_scheme.scheme_type == "custom":\n+ #if $type_of_scheme.scheme_input.is_of_type(\'fasta\'):\n+ ln -s \'$type_of_scheme.scheme_input\' custom_scheme.fasta &&\n+ #end if\n+ #end if\n+\n+ ## Start the actual command here\n+ hansel \n+\n+\n+ ## Select the scheme\n+ -s\n+\n+ #if $type_of_scheme.scheme_type == "heidelberg":\n+ heidelberg\n+ #elif $type_of_scheme.scheme_type == "enteritidis":\n+ enteritidis\n+ #elif $type_of_scheme.scheme_type == "custom":\n+ custom_scheme.fasta\n+ #end if\n+\n+\n+ #if $kmer_min\n+ --min-kmer-freq $kmer_min\n+ #end if\n+\n+ #if $kmer_max\n+ --max-kmer-freq $kmer_max\n+ #end if\n+\n+ ## Adding more parameters to the command.\n+ -vvv -t "\\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab \n+\n+\n+ ## Entering the file inputs.\n+ #if $data_type.type == "single":\n+\n+ #if $data_type.fastq_input1.is_of_type(\'fastqsanger\') or $data_type.fastq_input1.is_of_type(\'fastq\'):\n+ fast_q_single.fastq\n+ #end if\n+\n+ #if $data_type.fastq_input1.is_of_type(\'fasta\'):\n+ fast_a_single.fasta\n+ #end if\n+\n+ #else\n+\n+ ##use -p to declare using two files.\n+ -p fast_q_paired_1.fastq fast_q_paired_2.fastq\n+\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <conditional name="data_type">\n+ <param name="type" type="select" label="Specify the read type.">\n+ <option value="single">Single-end Data</option>\n+ <option value="paired">Paired-end Data</option>\n+ <option value="collection">Collection Paired-end Data</option>\n+ </param>\n+ <when value="single">\n+ <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/>\n+ </when>\n+ <when value="paired">\n+ <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>\n+ <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>\n+ </when>\n+ <when value="collection">\n+ <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />\n+ </when>\n+ </conditional>\n+ <conditional name="type_of_scheme">\n+ <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)">\n+ <option value="heidelberg">He'..b'-------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+\n+\n+\n+Contents of ``match_results.tab``:\n+\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | seq | freq | sample | file_path | tilename | is_pos_tile | subtype | refposition | is_kmer_freq_okay | scheme |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC | 68 | 564 | forward.fastqsanger; reverse.fastqsanger | 21097-2.2.1.1.1 | True | 2.2.1.1.1 | 21097 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT | 77 | 564 | forward.fastqsanger; reverse.fastqsanger | 157792-2.2.1.1.1 | True | 2.2.1.1.1 | 157792 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC | 67 | 564 | forward.fastqsanger; reverse.fastqsanger | 293728-2.2.1.1 | True | 2.2.1.1 | 293728 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+\n+ Next 200 lines omitted.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">@ARTICLE{a1,\n+ title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},\n+ author = {Genevi\xc3\xa8ve Labb\xc3\xa9, James Robertson, Peter Kruczkiewicz, Chad R. Laing, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},\n+ url = {https://github.com/phac-nml/bio_hansel}\n+ }\n+ }</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e3698ac146d7 test-data/SRR1002850_SMALL.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR1002850_SMALL.fasta Tue Oct 03 10:39:11 2017 -0400

b'@@ -0,0 +1,766 @@\n+>NODE_384_length_56_cov_34125_ID_767\n+CTAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTACTTTCTGACCTCGG\n+>NODE_383_length_56_cov_335_ID_765\n+CAATTGTGATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGCCCCGAAAA\n+>NODE_382_length_56_cov_201_ID_763\n+CCGTCGCTCACCGACGAAAGATAAAACGGAATCAGGCTAGCGGGGTGTCGGGGTGC\n+>NODE_377_length_57_cov_34097.5_ID_753\n+AAACCGAGGTCAGAAAGTACCGTCGCTCACCGACGAAAGATAAAACTGAATCAGGCT\n+>NODE_376_length_57_cov_200_ID_751\n+GAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTAGTGCCGCCAGGCAAATTCTTT\n+>NODE_375_length_58_cov_19568.3_ID_749\n+TAATACCGTCACACGCGACGCTATCACAATTGCCATCTGGTCAGGGGTGCACCCCGAC\n+>NODE_374_length_58_cov_29262.3_ID_747\n+GCACCCCGACACCCCGCTAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTA\n+>NODE_372_length_59_cov_291.25_ID_743\n+TAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGGACTTTCTGACCTCGGTTTT\n+>NODE_369_length_60_cov_34761.2_ID_737\n+GCGGTGGCCGAAACCCTGAAATATTCCACGAAGCCGGCTGACATGGTGGCCGATCCTGAA\n+>NODE_367_length_60_cov_167.2_ID_733\n+CCGAGGGCGACGATGACGGTTCACGAATCGCGTTCGAGTGGAAACCCGAGGTCAGAAAGT\n+>NODE_365_length_61_cov_228.5_ID_729\n+TCGCGTTCGAGTGGAAAACCGAGGTCAGAAAGTCCCGTCGCTCACCGACGAAAGATAAAAC\n+>NODE_360_length_62_cov_66.7143_ID_719\n+CAGGGGTGCACCCCGACACCCCGCTAGCCTGATTCAGTTTTATCTTTCGTCGGTGGGCGACG\n+>NODE_357_length_63_cov_202.375_ID_713\n+GGGGTGTGGGGGTGCACCCCTGACCAGATGGCAATTGTGATAGCGTCGCGTGTGACGGTATTA\n+>NODE_356_length_63_cov_142.75_ID_711\n+TGTAATTGTAATAACGTCACACGCGACGCTATCACAATTGCCATCTGGTCAGGGGGGCACCCC\n+>NODE_355_length_64_cov_127.667_ID_709\n+CGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAGCGGGGTGTCGGGGTGCCCCCCTGAC\n+>NODE_352_length_64_cov_30.6667_ID_703\n+CGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCACCCCTGAC\n+>NODE_351_length_64_cov_104.444_ID_701\n+ATGATATTTCCGAGGGCGACGATGACGGTTCACGAATCGCGTTCGAGTGGAAACCCGAGGTCAG\n+>NODE_349_length_64_cov_29.3333_ID_697\n+GTCAGGGGGGCACCCCGACACCCCCCTAGCCTGATTCAGTTTTATCTTTCGTCGGGGAGCGACG\n+>NODE_347_length_64_cov_32_ID_693\n+GTCAGGGGGGCACCCCGACACCCCGCTAGCCTGATTCAGTTTTTTCTTTCGTCGGGGAGCGACG\n+>NODE_346_length_65_cov_38729.2_ID_691\n+CTGACCTCGGTTTTCCACTCGAACGCGATTCGTGAACCGTCATCGTCGCCCTCGGAAATATCATC\n+>NODE_342_length_66_cov_28.1818_ID_683\n+CTGACCTCGGGTTTCCACTCGAACGCGATTCGTGAACCGTCATCGTCGCCCTCGGGAATATCATCA\n+>NODE_340_length_67_cov_71.3333_ID_679\n+CCGACGAAAGATAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCCCCCCTGACCAGATGGCAATT\n+>NODE_336_length_67_cov_56_ID_671\n+CTTGAATATGGCGGTGAGGGGGGGATTGACTCGCTTTGCTCGCCCCTTCGGGGCAGCCCGTTCGCTG\n+>NODE_335_length_68_cov_32300.2_ID_669\n+CCCCGACACCCCGCTAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTACTTTCTGACCTCG\n+>NODE_333_length_69_cov_126.429_ID_665\n+GGTGTCGGGGTGCCCCCCTGACCAGAGGGCAATTGTGATAGCGTCGCGTGTGACGGTATTACAATTACA\n+>NODE_332_length_69_cov_101.286_ID_663\n+GGTGTCGGGGTGCCCCCCTGACCAGATGGCATTTGTGATAGCGTCGCGTGTGACGGTATTACAATTACA\n+>NODE_327_length_71_cov_31.375_ID_653\n+GCACCCCGACACCCCCCTAGCCTGATTCAGTTTTATCTTTCGTCGGGGAGCGACGGTACTTTCTGACCTCG\n+>NODE_326_length_71_cov_108.125_ID_651\n+CCGAGGTCAGAAAGTCCCGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAGCGGGGTGTCGGGGTG\n+>NODE_324_length_71_cov_35.75_ID_647\n+TGTAATTGTAATACCCTCACACGCGACGCTATCACAATTGCCATCTGGTCAGGGGGGCACCCCGACACCCC\n+>NODE_318_length_74_cov_355.895_ID_635\n+GTAGGCGTTATTGGCGCAGCCAGTTTGGACACGGACAGCGCGCAAAAACCGGAGCGTACACGTAGTACGTGAGG\n+>NODE_316_length_76_cov_59.5714_ID_631\n+CGTCGCTCACCGACGAAAGAAAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCACCCCTGACCAGATGGCAATT\n+>NODE_315_length_76_cov_76.8571_ID_629\n+CGTCGCTCACCGACGAAAGATAAAACTGAATCAGGCTAGCGGGGTGTGGGGGTGCACCCCTGACCAGATGGCAATT\n+>NODE_314_length_76_cov_172.333_ID_627\n+AATTGCCATCTGGTCAGGGGTGCACCCCGACACCCCGCTAGCCTGATTCCGTTTTATCTTTCGTCGGTGAGCGACG\n+>NODE_313_length_76_cov_35231.5_ID_625\n+AAACGGCAAAATGATTTACTCGCCGTTTGTGTGGGTTGTTTTGTGGGGTGTCAATGGGGTTGTGGTCTTTTTTGTG\n+>NODE_312_length_76_cov_28.9048_ID_623\n+CGTCGCTCACCGACGAAAGAAAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCCCCCCTGACCAGATGGCAATT\n+>NODE_310_length_79_cov_105.5_ID_619\n+CTCAAAAAACCGAGAAACGGCGGGGATTTTCGGGACAGGATGTGTAATTGTAATAACGTCACACGCGACGCTATCACAA\n+>NODE_306_length_82_cov_64.2963_ID_611\n+TATCACAATTGCCATCTGGTCAGGGGGGCACCCCGACACCCCGCTAGCCTGATTCCGTTTTATCTTTCGTCGGTGAGCGACG\n+>NODE_294_length'..b'GGATGGCCGCGTCTTTGAAGCGCTACTGGTTGGCTCCGATTCGCTTACCGATCTGGCGGTGCTGAAGATCAACGCCACTGGCGGGCTGCCTACCATCCCGATTAATACAAAGCGTACACCGCATATTGGCGACGTCGTACTGGCTATCGGCAACCCATATAATCTGGGACAGACCATTACCCAGGGGATCATCAGCGCAACGGGTCGTATCGGCCTGAACCCGACGGGGCGACAGAATTTTCTCCAGACCGACGCCTCGATTAACCACGGTAATTCCGGCGGCGCGCTGGTCAACTCGTTAGGCGAACTGATGGGGATCAACACCCTCTCTTTTGATAAGAGTAACGATGGTGAAACGCCGGAAGGCCTTGGTTTTGCGATTCCCTTCCAGCTAGCCACGAAAATTATGGATAAGCTTATCCGCGACGGTCGTGTGATTCGCGGCTATATCGGTATTGGCGGACGAGAAATCGCGCCGCTGCACGCGCAGCAGGGTAGCGGCATGGACCCGATTCAGGGCATTGTCGTTAATGAAGTGACGCCAAACGGCCCCGCCGCGCTTGCCGGTATTCAGGTTAATGATTTGATTATTTCGGTCAATAATAAACCCGCCGTGTCCGCGCTGGAGACAATGGATCAGGTGGCGGAAATCCGCCCGGGCTCCGTCATTCCGGTCGTGGTAATGCGGGATGATAAGCAACTCACGTTCCAGGTGACGGTGCAGGAATACCCGGCGTCGAACTAAAACGACGCGGCTTTTGCCTGCGTCGTTCGACGGCTAGTCAATAAAGACTGGCCCTGCCGGAAAATGCGCCAGGAAACTCGTGAAGATCAGCAGAGCGGGGAGACTTTTCTCCCCGACGGCTTCTTCACGCAGCGCCTTATCCAGTGCAAGCAGGCTGTGCTCCCCCCCTTCCCCCAAAATGCCGCCCATCCAGAGCAGTCGTTGCGCCTGTTGACGCGCATACTGCGATGCGCTTTTCCAGGCGACCAGATGCAGCAACGTTTGTAACAGCAGGACCCGAGACGCGTGACCATCGCGTTGCAATCGCCTGAATACGGGTAATGCAATACTACGTACCGTCGAGAAACCGCTCGCCGCCTCCCCCTCAATCGGCGATAAACCAACAGCCGCCTGTTTGACGAAATCGCATAACTGATTGTGTGTTAATGGCCGCTCGCCTGCGCTCATATACCCTGCGGCAAAACAGAGTAACCCGATACCCTGAGCCCAATCGGTCGATGGCAGAATCCCCTGCGGAACATTCGGTGCCGACGTCTGTGCGGCACAAAGCCCCTCGTCGTAACACTGTGCAAAACGTTGCTCATATATTGCTGAGTTGATGCCAGACCACGGCAGTAAATGCAGCGCTGGCTCAAGCTCAGTTATCTGATTCACCGTCTCAACAACATAACGCAAGATGGTTTCTCTGGATGGCATGGATGTACCTTGCCGAAACGCAACCATTTCACTCATTACTGTGTCCTCATTTTGCGGGAGCAGAATCACTGCTCCCGATTAGATTGGATTACATTGCCAGCACGTACTTCAGCATCACGCCCGCCGCAATGGCCGAACCGATAACCCCCGCCACGTTCGGGCCCATCGCGTGCATCAGCAGGAAGTTCTGCGGGTCCGACTCCAGGCCCACCTTGTTCGATACGCGGGCCGCCATCGGCACCGCCGACACCCCCGCCGAACCGATAAGCGGGTTGATTTTGTTCTTACTGCACAGGTTCAGCAGCTTCGCCATCAGCACCCCGGCGGCAGTCCCGATACCAAAGGCAATCACACCCAGCAGCAGAATGCCCAGCGTCTGCGGCTGCAGGAACTTGTCCGCCACCAGCTTCGCCCCTACCGACAGCCCGAGGAAAATGGTGACGATGTTGATCAGCCCGTTCTGCACTGTGTCGCTCAGGCGCTCCACCACGCCGCTTTCACGCATCAGATTGCCGAAGCAGAACATCCCCAGCAGCGGCGCGGCGTCCGGCAGCAGCAGCGCCACCAGTAGTAACAGCACTACCGGGAAGAGGATTTTTTCCCGCTTACTCACCGTGCGCAGCTGCACCATGCGGATTTTCCGCTCCGTCTCCGTGGTCAGCGCGCGCATAATCGGCGGCTGGATTAACGGCACCAGCGCCATATACGAGTACGCCGCCACCGCGATGGCCCCCAGCAGCTCCGGCGCCAGTTTGCCCGACAGATAAATGGCCGTCGGACCGTCCGCGCCGCCGATGATGCCTATCGCCGCCGCCTGCGGCAGGGTGAAGGAAATCAGGCCGAAGTAATTCAGCGTCAGCGCCCCCAGCACCGTGGCGAAGATGCCGAACTGCGCCGCCGCGCCGAGCAGCAGGGTACGCGGGTTGGCCAGCAGCGGGCCGAAGTCGGTCATCGCGCCGACGCCCATAAAGATGACCAGCGGCGCGACGCCGGAGCCAATCGCCACTTTATAGAACAGCGCCAGCACCCCCGGCGTGTAGCCCATGTCCACCGCCAGGTTCTCCATCTGGCTCTGAACGGAGGGCAGCGCCAGCGCTAACGCCTCCTTGATGGCGTGCACGTCCGGCGCGCAGTTAAGCTTCGCGGCAATCACCGCCAGCTGCCCGGCGTCGTGGTGCGCCAGCAGGCTTTCCAGCGCGGTCAGCGCCATGCCCGCTTCCGGGATGTTGGAGAGCAGGCCGCCGAAGCCAATCGGCAACAGCAACAACGGCTCGAACTTTTTCGCAATCGCCAGCCACAGCAGCAGCAGGCTGACCAGCAGCATGATGGCCTGGCCTGCGCCAAGGTGCATCAGCCCCATGCCCTGAAGCAGGGCGTTCAGACTTTCCATTCGTCCTCTCCGTTACGCAAGCTGCATCAGGGTGTCGCCCACCGCCACCGCATCCCCGGCTTTCACCGCGATGCCGCGTACCGTCCCGGCCTGCGCGGCGCGGATTTCGGTTTCCATTTTCATGGCTTCCAGAATCAGCAGCACATCGCCTTCGGCCACCGTCTGGCCTTCCGTCGCCACCACTTTCCAGATATTGCCCGCCAGCGGCGCGCTGACCGGGGTGCCCGCGCCCGCCGGGGCGGCGGCAGGCGCCGCGGTCTGAACCGGCGCAGAACTGGCCGTGGCCAGCTGGCTGATATCGCCGCCGTCGCTGACTTTCACCACAAAGGCTTTGCCTTCCACTTCGACGGTGTAGATACCGGAAGCGGCGGGTTTTGCGGCTTTTTCCTCTTTCACGGCAGGTTTCGCGGCTTCCGCCTGCGGCAGTGGCTCAAACGCCGCCGGGTTATGGCGGTTTTCGAGGAATTTCAGCCCGACCTGCGGGAACAGTGCCACGGTGAGGACGTCATCAATGGCGTTCTCTGCAAGCCGGATGCCTTTTTCTGCCGCCTGGCGTTTAATGTCCGCTTCCAGTTGCGCCAGTTCCGGTTTCAGTAAATCCGCCGGGCGGCAGGTGACGGCCTCTTCGCCGTCCAGCACTCTGGCCTGTAACGCCGCGTTGACCGGCGCTGGCGTGTGGCCGTATTCGCCCTTCAGTATCCCGGCGGTTTCTTTGGCGATGGTTT\n+>NODE_216_length_189_cov_23403.1_ID_431\n+CCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTACTTTCTGACCTCGGTTTTTCACTCGAACGCGATTCGTGAACCGTCATCGTCGCCCTCGGAAATATCATCACCGATCACCATGTCGGCGTCAGTTTCCTGATCGAGTTTCAGCACGTCTTTGAGTGCGCCGCCGGTCGCCACAAAGCGGCGC\n+>NODE_222_length_167_cov_18131.6_ID_443\n+CACTCAAAGACGTGCTGAAACTCGATCAGGAAACTGACGCCGACATGGTGATCGGTGATGATATTTCCGAGGGCGACGATGACGGTTCACGAATCGCGTTCGAGTGAAAAACCGAGGTCAGAAAGTACCGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAG\n'

diff -r 000000000000 -r e3698ac146d7 test-data/SRR5646583_SMALL_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL_1.fastq Tue Oct 03 10:39:11 2017 -0400

b'@@ -0,0 +1,20000 @@\n+@32927/1\n+GTGAGTAAGTTGCGCGATATTCTGCTGGATTCGGTAGTAACCAGCTCTATTGTTCTCTTACTGGTCGGCTGCTCAATGGGAATGTCATGGGCGATGACCAATGCCGATGTTCCTGAACTGATTAATGAAATGATTACCAGCGTGTCCGAAA\n++\n+AAA?ADD5F5BFGGGCCFFGGGGHHGHHHGFFFHGHGHHGCHHHHFHGHHGHEGHFHHHHHFHHHG?AEGGGEHHFGFGHGHFHFFFHHHHHGGGCHHHFGHFHHGCGFFGFGHHHHHGHHHHHBGFHHHHHGFHHFFHGHFED<FFD?ED\n+@351952/1\n+GGATTACCAGGAAGTGCTGGAAGAGTTTAACGAACATCGTAATGAGCCTGTTGATACTAACGACTTTATTGAGGCGATTGAGCGAAGTAAACGTCGCTTCCATGTTGTTGAAAATGAACAGGAGCTACTGCAAATGCTCAATGCGCCA\n++\n+CCCCCFFFBFCBFGFGFGGGGGHHHHHHHHHGGFGGGHGHHHDHHHHHHHHHHHGHHHHHHFFGGGHHHHGHFHGGGGHGHGHGGGGFGHHHGHHGGGGGGHHHHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHGHGGHHHHGGGGG\n+@37856/1\n+GCGCAGGAACGTATCGGCTTACCGTACCGGTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAG\n++\n+CCCCCCCCFFCBG5GGGGGGGGHGGHGGGGGGGHHHHGGGGHHGHHHHHHHHGHHHGGGGGGGHHHHHHHHHHHHHHHHHGGGGGGGGGGHHHHHGGGGGGGGHGGGGGGGGGGHHHHHGGHHHHHHHHHHHHGGGGGHHHGHHGHHHHHF\n+@844740/2\n+GATCATGATTAGTCGTGCTCAAAGCGGGCCCCCACTCTACAAGTTGCAAAATTTGTTACGGGTAACTGTTATCGGTAACATTGTCCAACCGCACCATTCACGACGCAATGACCATTCGTGCCAAAAGTGAATAAGTGTGAGCTACTTCAAA\n++\n+BBBBBFFFFFFFGGFGGGGGGGGHGGGFGGGGGCFCGHHHCHHHHFFGHHFHFHHFFFHGGGEEHHHHHHHFHHGAHGHHGHFHHHHHHGGGGFFAGHFFFEGGGGCCFFFGHHHFHFFFGHHHHEHGHFFHFFF1GDFF<GHHEHFHEGG\n+@1034303/1\n+CCTGAATATTCATCATCAAACTACCGTCGCCGGAAAAACACAGCACCTTGTTGCCCGGATTCGCCAGCGCCGCGCCAATCGCCGCGGGCAGACCAAACCCCATGGTGCCCAGCCCGCCGGAAGTCAGCCACTGACGCGGACGGTTGAGCGG\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHGGGGGGGGGGGHHGHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGGGGHHGGGGGGGGGGGGHHHHGHGGGGHGHFGFHHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFF\n+@79331/2\n+CCCTGGTATTCGACGTAGAGCTGCTGGATATCAAACCAGCGCCGAAAGCGGATGCTAAACCTGCCGATGCGGCTGACGCTAAAGCCGCAGATGCTGCTAAAAAATAAAAACTGAGAGCCGCCGCTTGTAATAGCGGCGGTTTTTTTTTTTT\n++\n+AAABCCFFFFFFGGGGGGGGGGHGHGGHGHHHHHHGGHHHGGGGGGGGHGGGGGGHHHHHFHHHHGGGGGGGGGGFHGGGGGHHHHGGGGGHHEGHHHHHHHHGHHHHHHGHHHHHHHHGGGGGGGGHHEHHHGGGGGG-;AEGGGAFF--\n+@234915/1\n+CACCTAATTTAACGGTCTGGTGACCAGAACCGACCGCACGCAAAAGCTTCTGAACCGATGAGGATGCTATGGGAAACACAACAATACAAACACAGAGTTTTCGTGCTGTGGATGCAGAGCAAAGCAAAAGCAAGCGCTACATTATTCCATT\n++\n+DDCDCFFFFFFFGGGGGGGGGGHHHGHHHHHGGGGGGGGGGGGGHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHGHHHHHHHHHHHGHGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHFGGGGHHHHHHHHHHH\n+@238890/1\n+GTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAGCGCGCGTCTGATGATTGACGCCCCTGCG\n++\n+BBCCCFFCCBCCGFGGGGGGGGHHHHHGGGGGGGHHHHHHHHHHHHHHHHHGGGGGGGGGGHGHHHGGGGGGGGHGGGGGGGGGGHHHHHHHHHHHHHHHHHHHGGGGGHHHGGHGHHHHHHGGGGGGGGGGHHHHHHFHHFGGGGGGGG\n+@238964/2\n+ATCGGCAGACAGGATACCTGGACCTGCGCGGCGGCATCGCCGGATTGCAGCGTAACGGTAAAAGAGGACTTGACTGGCGCGATTTGCATCTCATCATTCGCCAGTACCGGTACGGTAAGCCGATACGTTCCTGCGCTAAGATCGCTTATTG\n++\n+AAA3AB?DBFBFCGGGGGFBFFHHHHFFGGGGGCFGGHGGGGGGGGHHHGHGGGGGGGG/CGHHGHGHHHHHHGHHHHFGGFCHGHGEHGHHHHHGGEFFDGGGCFHFGC<-CAGBAEFHGG?@CCGHHH/GFECGCBCFGGF.DACEFF0\n+@135672/1\n+GAATACGGTCATATTGATATTCTGGTGAATAACGCGGGTTTGATCCGTCGTGAAGATGCGATTGATTTCACGGAAAAAGACTGGGATGACGTCATGAACCTGAACATCAAGAGCGTGTTCTTTATGTCTCAGGCGGCGGCAAAACTTTTTA\n++\n+BA@AAFBAFB?FGGGGFGGGGGHHFB4FGGFHGGGGGGEFGDHHHGHFGGGGHGHFFHHGGHHGGHFFHHHHGGGGGFGGHHHHEHHGHHGFEFHGGHHFFHHGFHHHFFFFHHC/CEFHHHHGHHHHBGHHHGCCCD-@DCAFEG0GG0.\n+@1027688/2\n+GTCTTCTATGTTACCGTCAATCAACCCGGAACTGGCCCGTATCGCTCCCGGCTTTCGTGCATTAATTATTAATGTTATTGCCGCTCCGATTCGCGATGCGCAGGTCGGAGCAATCGCGCTAAAAGAGGCCTGTCAGGCCGTATTTAACGGG\n++\n+>A11>333F33DEGGGFE1EF111BAAA000A1B0FBEEAEFG//0/A//A/EA01/0??EF211222B2222BGFH2@111/E///?EE/1>?//<<E/////0B<B@?/<0FHEECCC?CHG1.0<.<1.0/00CHC-<<.:CFHH.@.\n+@278520/1\n+GTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAGCGCGCGTCTGATGATTGACGCCCCTGCG\n++\n+BABBBFFBBBBBGGGGGGGGGGHHHHHGGGGGGGHHGHHHHHHHHHHHHHHGGGGGFGGGGHHHHHGGGGGGGGHGGGGGGGGGGHHHHHHFGHHHGHHHHHHGGCGGGHHHGGFDEHHHHHGGGGGGGGGGHHHHHHHHHGGGGGGGGG\n+@1088790/2\n+GCTCCGGCGTGGTAACGGCATTCGCCTGCTCGCTGGTCCGCGTCGCGGCAAGCCACGGGAAAACGGTCGCATCACACTGGTCTGGTAAAGGCAGATCCGCAGTATCCTGCGGCATCACGTTGAGCCACAGCTTGCGC'..b'CGGG\n++\n+1>AAAF@>AABBFFBFEFGBGGH0A3EAEEAEA0/E///AE//0AEGCECGHHF1GEEECEGFBCGFBF111E/>EF>GBE/EECCGFCC?/CCECGCCFH??-<@?EH0EECGHH.@@-:CCG/.-@---;-;-BAA=@-@@??F?F-99\n+@47237/1\n+ATGGAATTAATTGGACTTAGTGAGAAGTGTTCATGGTGTCCCCTGCAGGAATCGAACCTGCAACTAGCCCTTAGGAGGGGCTCGTTATATCCATTTAACTAAGGGGACAACGCGGCGCCAGTATAGCGTTTTTTATTCGCCGGAGTAAGTG\n++\n+ABBBAFFFFFFFGFGGGGGGGFFHHHHHHGGHHHHFGHHHHHHHGHHHGGHGHHHHHGHHHHHHGHFHHHHHHHHHHGGGGCHFFEHHHHHHGHHHHHHHHCFEGGEGGHHFGGGGGGD/B?GFHHHGGGGGGGHHFHFGFCGDCGHHHFH\n+@1474189/1\n+TGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATAATCCTTAGCATCTGCTAAGGATTTTTTTTTGCCTAAAATTACCTGATTATCTGATCAGGTAATCGTAAGTTCCCTTCTTTTTCTT\n++\n+AABAB5DFBFFBGAEEEGGGGGGEEECGE?EEHHGHGEHFDGHEGHHHECEGDEEFGFCGFHEEG4FGHHHFG3FFFBGHHHGHFB3FHHFFEGGGGFHHHH11DGHHHHH0FBFG2FGHHFG<GFG2F</G0?<FF1FDDFFDGGGHBGH\n+@343204/2\n+CTAAGGAGGCATTCAGTGCGGATTCATATTCTCTTTGACCTCAATTTCCCTGGTCAGTTTCCCCATTCGTCCAGAAATGCTCCCTGCGCTCCGCCATGCGCACTAATTGTTCACAAGGCGCGTAACGAGGACCGTAAAGTGCGGCCAGGCG\n++\n+3ABBBFFA??AFGFFGGGGGGGGGCFHFHHHGHHHHHHFHHHHHFFBGHHGGHHHHHHGGHHHHHHEHHHGGGGHHHGFFHFHEHHGECFGEDEFCAGFEF?EECBGBFGHHGGFFGAGGGGDDDGGGFGGHHCCGDGFFGHGGFGCE.CC\n+@707874/1\n+GATTAAGCAACTGCTCGACGTCGGCGCGCAAACGCTTCTGATACCGATGGTGCAGAATGCCGATGAAGCGCGAAACGCCGTAGCGGCTACGCGTTATCCGCCTGCCGGTATTCGCGGCGTGGGCAGCGCGCTGGCGCGGGCATCGCGCTGG\n++\n+A>AAAFFFFF?FGFGGCG1EEF0EEEGGCGFECE/F/A1DGHGD1EFC/E@FGFEDC1@1@E>EEFGHHECEGGC@C//C</CF??//<FC/<CCCHGHCACCEAGCG--CGBC.A--@-??AEFGGG;9@@?=B-:@@@?>F/9A---;@\n+@737981/2\n+GATTAAGCAACTGCTCGACGTCGGCGCGCAAACGCTGCTGATACCGATGGTGCAGAATGCCGATGAAGCGCGAAACGCCGTAGCGGCTACGCGTTATCCGCCTGCCGGTATTCGCGGCGTGGGCAGCGCGCTGGCGCGGGCATCGCGCTTG\n++\n+>11A1F1DFFF1BGFCEGG0EE0A0E?/EE//B/A/E?1111@F1/?@??1FBBF10BBD1>E//BF1@>//></</E///<///<B@C0<//>CCEHE..<..<.<--::CH/.;@@G?A-A.B.CA@@<---9;A-----;/A-@=---\n+@156200/2\n+GTCATACAGCGGCGTTGACGGCCAGGTCTGATCAACCAGTTCGCTGCCTTCATCGCTGGCGATCAGGAATCCGCCGGGAGCGGGGCTATTCAGCGACTGGGCGGCACGCGCGGTCTCGCGAGAAATAAACGGCGCCGTTGAGGTCGTGAC\n++\n+CBABCFFFFFCCGGGGGGGGEGGGHCGHHHGHHHFGHGGFHHGGGGGHHGHHGHHGHGGGGGGGGGHHEHHHGGGGGG//DGC?FGGEHFHGFHGGFCGHHHGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFF@FFFEF/BABFFF\n+@530652/2\n+ACCTTATCAGGCCTACATAAGCACTCGGCTGGTAGGCCTGATAAGCGCAGCGCCATCAGACATTGATTGGCAATTAAGCCTGTTTAGCAGCTTCTGCTGCTTTCACGATCACCGCGAAGGCGTCAGCTTTCAGAGAAGCGCCGCCTACCAG\n++\n+BBCCCFFFFFFFGGGGGGGGGGHHHHGGGGGGHHHGHHHGHHHHHHGGGGGGGGGGGHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHCGFGHHGGGEGGGHGGGGGHHHHHHHGHHHGGGGGGGGGGGHHH\n+@424544/1\n+ACTACGAATACGGCGCAGCGGGCGACCGTTTTCATCAAATTCCGGTGAAATGACGTCGTTTTTCATAAAAGTGTAGTCTGCTGTGTTTGAGTTCTGAAAACGGGCATTATCCAAAGTTAGTTGCCGGATGCAAGCATGAAGCGCACTGCGG\n++\n+DDCCDDCCCDFCGGGGGGGGGGGGGGGGGGHGHHHHHHHHHHHHGGGGHHHHHHGGGGGGGGGHHHHHHHHHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHGGGGGHHHHHHHHHGHHGHHHHHHGGGGGHHHHHHHHHHHGGGGGGHGGF\n+@788695/2\n+CTGCTGGTGGTTGAGCCGCCCTATGATCCTGAGTTGGACTTTCATTACCGCATCTTCAACGCCGACGGCAGTGAAGTCTCGCAGTGCGGCAATGGCGCGCGCTGTTTCGCGCGATTTGTTCGCCTGAAAGGGCTAACCAATAAACGCGACA\n++\n+BBBBBFFFF@ABGGFGGGGGGGGHHHHHHHGHHHHHHHHHHHHHHHHHHGGGGGHHHHGHGGGGGGGGGCGGHGHHGHHHHGGGGHHEGGGGHHHHGGGGGGGGGHFHGGGGGGGHGHHHHGGGGHHEHHGGGGFHHHHHGGGGGGGGGC-\n+@1399297/2\n+TTCATACAGAGATCATGACCACACATGCAACAAAAAAGCCTGCAACTCATTGAAGTTACAGGCTTTTTTAAGGTTCATGATGCATCATGAATGAATGTTTGGTGGAGCTGGCGGGAGTTGAACCCGCGTCCGAAATTCCTACATCCTCGGT\n++\n+AAABBFFFFFFCGGGGGGGGFGHGGHGHHCHHHHHHGGHGHHGHHHFFFHGHHFHGHHHHHEGHHHGHGHFHG@GFHHFHHGHFHHHHHHHHHHHHHHGHHG?FFEEFEFBE?CCCGDFFHHGFDFC@DGG@DGG.1>GG11<F0GGFGD<\n+@52275/1\n+GTCACAGTCGACGTTGGCCCCCAAATCAAGCACTACCGTTTTGCCCTTTTGCTGGTGCGGTAATACCGTCACCAACGCCGGACGCTCAATCCCCTCAAGAGGCTTGAGCAATAATTTCGCCAGCCCCATCAGCGCCCCGGTATTACCGGCG\n++\n+BBBBBFFDFA?DCEGGGGGGGGGCHHHHHGGFHHHGHGGGHGHHHHHHHHGGHHHHHH?EE?FHHHHGFFDGHHHGDGG@ECGGGDGGEHHHHGHGHHHBCHGHHCHHGFBGHHHHHHHGGGFGGGGGHHHHHGGCC?GCC-EHHEHFFG?\n+@384298/2\n+GTGTTTACACAGGAGCTGCTCCAGTTCGCTTAATGACGCCACAGTCCAGGTTGGATGAATACCCGCGGGCTGCTCGCGATGATGCGCGTTAAGCCAGCAGGTCGACAGCCCGGCGTTAATGCCGCCAAGAATATCGGATTCCGCGGTATCG\n++\n+AAABBFFFFFFFGG2GGGGGGGHHHHGGGGHGGHGHHGGGGGHHHHFHHGCGHGFHHHHHHHHHGGGGGGGGGHHGGG?FGHHHHFGGGGGEHHHHHGHFG0FCCGGGEHGGFDFCFGGGHHHFC?:@CGHBGFHGCD.EBFFGDA.9EF.\n'

diff -r 000000000000 -r e3698ac146d7 test-data/SRR5646583_SMALL_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL_2.fastq Tue Oct 03 10:39:11 2017 -0400