# HG changeset patch # User iuc # Date 1637790734 0 # Node ID fa3c3a64c99311375f684283286976fc887c6b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644" diff -r 000000000000 -r fa3c3a64c993 blast2rma.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast2rma.xml Wed Nov 24 21:52:14 2021 +0000 @@ -0,0 +1,246 @@ + + from BLAST output + + macros.xml + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Computes MEGAN RMA files from BLAST (or similar) files. Inputs consist of reads in fasta or fasqsanger format (gzip compressin +is supported) and associated Blast files. Each read file should have been used previously as the Blast input to produce the +associated Blast file for this tool. + +This wrapper supports the following formats for the input Blast file. The SAM, Tabular and Text formats can be produced by +The Galaxy MALT Analyzer tool. When these formats are used, this tool will apply the SAM, BlastText and BlastTab format options +required by MEGAN. + + * **Direct Access Archive (DAA)** - a proprietary file format developed by PowerISO Computing for disk image files + * **BlastXML** - XML output from Blast + * **Sequence Alignment/Map (SAM)** - a tab-delimited text format consisting of a header section, which is optional, and an alignment section + * **Tabular** - information presented in the form of a table with rows and columns + * **Text** - plain text format + +This tool outputs a RealMedia Audio (RMA) file. MEGAN uses an update of the original RMA file format known as RMA6. This update +requires less disk space for files. + + + https://doi.org/10.1101/050559 + +
+ diff -r 000000000000 -r fa3c3a64c993 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 24 21:52:14 2021 +0000 @@ -0,0 +1,71 @@ + + 6.21.7 + 0 + 20.09 + + + megan + + + + + megan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1101/gr.5969107 + + + + diff -r 000000000000 -r fa3c3a64c993 test-data/13-1941-6_S4_L001_R1_600000.fastq.gz Binary file test-data/13-1941-6_S4_L001_R1_600000.fastq.gz has changed diff -r 000000000000 -r fa3c3a64c993 test-data/13-1941-6_S4_L001_R2_600000.fastq.gz Binary file test-data/13-1941-6_S4_L001_R2_600000.fastq.gz has changed diff -r 000000000000 -r fa3c3a64c993 test-data/blast_R1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast_R1.txt Wed Nov 24 21:52:14 2021 +0000 @@ -0,0 +1,404 @@ +BLASTN output produced by MALT + + +Query= XXXXXXXXXX:7:1101:1582:1835#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1610:1859#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1743:1871#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1878#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2990:100153#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1624:1906#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1666:1926#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2921:100163#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1513:1929#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2759:100170#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1708:1937#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2981:100211#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1688:1946#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2767:100225#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1959#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2797:100234#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1552:1976#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1748:1978#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2779:100239#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1593:1980#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2946:100242#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1987:1781#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3046:100006#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1900:1788#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3214:100027#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1848:1879#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3237:100032#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3027:100049#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1756:1891#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3238:100065#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1915:1901#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100082#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1964:1931#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3088:100091#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1840:1948#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3105:100094#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1958:1952#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3190:100106#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1993:1999#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3117:100110#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2159:1798#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3147:100111#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2152:1838#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3065:100152#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2180:1843#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3154:100159#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2125:1861#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100173#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2076:1911#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3166:100190#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2196:1920#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3225:100207#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2115:1927#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3019:100219#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2179:1937#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3202:100230#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2149:1945#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3211:100242#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2169:1964#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3168:100244#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3005:100246#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2313:1789#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3253:100014#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2361:1794#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2337:1794#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3284:100039#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2477:1795#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3310:100056#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2355:1821#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3420:100060#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2418:1834#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3267:100061#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2378:1838#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3416:100083#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2481:1853#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3411:100111#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3258:100128#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2252:1856#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3428:100129#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1871#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3387:100138#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2269:1904#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3444:100163#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2259:1943#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3371:100179#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2371:1957#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3311:100186#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1961#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3438:100192#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2333:1962#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3479:100209#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2459:1990#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3417:100210#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2372:1994#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3452:100214#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2677:1830#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3354:100219#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2603:1846#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3600:100019#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2535:1848#/1 + +***** No hits found ****** + +EOF diff -r 000000000000 -r fa3c3a64c993 test-data/blast_R2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast_R2.txt Wed Nov 24 21:52:14 2021 +0000 @@ -0,0 +1,404 @@ +BLASTN output produced by MALT + + +Query= XXXXXXXXXX:7:1101:1582:1835#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1610:1859#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1743:1871#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1878#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2990:100153#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1624:1906#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1666:1926#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2921:100163#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1513:1929#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2759:100170#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1708:1937#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2981:100211#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1688:1946#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2767:100225#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1959#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2797:100234#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1552:1976#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1748:1978#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2779:100239#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1593:1980#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2946:100242#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1987:1781#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3046:100006#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1900:1788#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3214:100027#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1848:1879#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3237:100032#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3027:100049#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1756:1891#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3238:100065#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1915:1901#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100082#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1964:1931#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3088:100091#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1840:1948#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3105:100094#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1958:1952#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3190:100106#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1993:1999#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3117:100110#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2159:1798#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3147:100111#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2152:1838#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3065:100152#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2180:1843#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3154:100159#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2125:1861#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100173#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2076:1911#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3166:100190#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2196:1920#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3225:100207#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2115:1927#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3019:100219#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2179:1937#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3202:100230#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2149:1945#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3211:100242#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2169:1964#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3168:100244#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3005:100246#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2313:1789#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3253:100014#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2361:1794#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2337:1794#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3284:100039#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2477:1795#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3310:100056#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2355:1821#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3420:100060#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2418:1834#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3267:100061#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2378:1838#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3416:100083#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2481:1853#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3411:100111#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3258:100128#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2252:1856#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3428:100129#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1871#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3387:100138#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2269:1904#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3444:100163#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2259:1943#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3371:100179#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2371:1957#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3311:100186#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1961#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3438:100192#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2333:1962#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3479:100209#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2459:1990#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3417:100210#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2372:1994#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3452:100214#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2677:1830#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3354:100219#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2603:1846#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3600:100019#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2535:1848#/2 + +***** No hits found ****** + +EOF diff -r 000000000000 -r fa3c3a64c993 test-data/contaminants.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contaminants.txt Wed Nov 24 21:52:14 2021 +0000 @@ -0,0 +1,12 @@ +Illumina Single End Adapter 1 ACACTCTTTCCCTACACGACGCTGTTCCATCT +Illumina Single End Adapter 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT +Illumina Single End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Single End PCR Primer 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT +Illumina Single End Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT + +Illumina Paired End Adapter 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Paired End Adapter 2 CTCGGCATTCCTGCTGAACCGCTCTTCCGATCT +Illumina Paried End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Paired End PCR Primer 2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT +Illumina Paried End Sequencing Primer 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Paired End Sequencing Primer 2 CGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT diff -r 000000000000 -r fa3c3a64c993 test-data/kegg_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kegg_output.txt Wed Nov 24 21:52:14 2021 +0000 @@ -0,0 +1,100 @@ +XXXXXXXXXX:7:1101:1582:1835#/1; ; +XXXXXXXXXX:7:1101:1610:1859#/1; ; +XXXXXXXXXX:7:1101:1743:1871#/1; ; +XXXXXXXXXX:7:1101:1536:1878#/1; ; +XXXXXXXXXX:7:1101:2990:100153#/1; ; +XXXXXXXXXX:7:1101:1624:1906#/1; ; +XXXXXXXXXX:7:1101:1666:1926#/1; ; +XXXXXXXXXX:7:1101:2921:100163#/1; ; +XXXXXXXXXX:7:1101:1513:1929#/1; ; +XXXXXXXXXX:7:1101:2759:100170#/1; ; +XXXXXXXXXX:7:1101:1708:1937#/1; ; +XXXXXXXXXX:7:1101:2981:100211#/1; ; +XXXXXXXXXX:7:1101:1688:1946#/1; ; +XXXXXXXXXX:7:1101:2767:100225#/1; ; +XXXXXXXXXX:7:1101:1536:1959#/1; ; +XXXXXXXXXX:7:1101:2797:100234#/1; ; +XXXXXXXXXX:7:1101:1552:1976#/1; ; +XXXXXXXXXX:7:1101:1748:1978#/1; ; +XXXXXXXXXX:7:1101:2779:100239#/1; ; +XXXXXXXXXX:7:1101:1593:1980#/1; ; +XXXXXXXXXX:7:1101:2946:100242#/1; ; +XXXXXXXXXX:7:1101:1987:1781#/1; ; +XXXXXXXXXX:7:1101:3046:100006#/1; ; +XXXXXXXXXX:7:1101:1900:1788#/1; ; +XXXXXXXXXX:7:1101:3214:100027#/1; ; +XXXXXXXXXX:7:1101:1848:1879#/1; ; +XXXXXXXXXX:7:1101:3237:100032#/1; ; +XXXXXXXXXX:7:1101:3027:100049#/1; ; +XXXXXXXXXX:7:1101:1756:1891#/1; ; +XXXXXXXXXX:7:1101:3238:100065#/1; ; +XXXXXXXXXX:7:1101:1915:1901#/1; ; +XXXXXXXXXX:7:1101:3198:100082#/1; ; +XXXXXXXXXX:7:1101:1964:1931#/1; ; +XXXXXXXXXX:7:1101:3088:100091#/1; ; +XXXXXXXXXX:7:1101:1840:1948#/1; ; +XXXXXXXXXX:7:1101:3105:100094#/1; ; +XXXXXXXXXX:7:1101:1958:1952#/1; ; +XXXXXXXXXX:7:1101:3190:100106#/1; ; +XXXXXXXXXX:7:1101:1993:1999#/1; ; +XXXXXXXXXX:7:1101:3117:100110#/1; ; +XXXXXXXXXX:7:1101:2159:1798#/1; ; +XXXXXXXXXX:7:1101:3147:100111#/1; ; +XXXXXXXXXX:7:1101:2152:1838#/1; ; +XXXXXXXXXX:7:1101:3065:100152#/1; ; +XXXXXXXXXX:7:1101:2180:1843#/1; ; +XXXXXXXXXX:7:1101:3154:100159#/1; ; +XXXXXXXXXX:7:1101:2125:1861#/1; ; +XXXXXXXXXX:7:1101:3198:100173#/1; ; +XXXXXXXXXX:7:1101:2076:1911#/1; ; +XXXXXXXXXX:7:1101:3166:100190#/1; ; +XXXXXXXXXX:7:1101:2196:1920#/1; ; +XXXXXXXXXX:7:1101:3225:100207#/1; ; +XXXXXXXXXX:7:1101:2115:1927#/1; ; +XXXXXXXXXX:7:1101:3019:100219#/1; ; +XXXXXXXXXX:7:1101:2179:1937#/1; ; +XXXXXXXXXX:7:1101:3202:100230#/1; ; +XXXXXXXXXX:7:1101:2149:1945#/1; ; +XXXXXXXXXX:7:1101:3211:100242#/1; ; +XXXXXXXXXX:7:1101:2169:1964#/1; ; +XXXXXXXXXX:7:1101:3168:100244#/1; ; +XXXXXXXXXX:7:1101:3005:100246#/1; ; +XXXXXXXXXX:7:1101:2313:1789#/1; ; +XXXXXXXXXX:7:1101:3253:100014#/1; ; +XXXXXXXXXX:7:1101:2361:1794#/1; ; +XXXXXXXXXX:7:1101:2337:1794#/1; ; +XXXXXXXXXX:7:1101:3284:100039#/1; ; +XXXXXXXXXX:7:1101:2477:1795#/1; ; +XXXXXXXXXX:7:1101:3310:100056#/1; ; +XXXXXXXXXX:7:1101:2355:1821#/1; ; +XXXXXXXXXX:7:1101:3420:100060#/1; ; +XXXXXXXXXX:7:1101:2418:1834#/1; ; +XXXXXXXXXX:7:1101:3267:100061#/1; ; +XXXXXXXXXX:7:1101:2378:1838#/1; ; +XXXXXXXXXX:7:1101:3416:100083#/1; ; +XXXXXXXXXX:7:1101:2481:1853#/1; ; +XXXXXXXXXX:7:1101:3411:100111#/1; ; +XXXXXXXXXX:7:1101:3258:100128#/1; ; +XXXXXXXXXX:7:1101:2252:1856#/1; ; +XXXXXXXXXX:7:1101:3428:100129#/1; ; +XXXXXXXXXX:7:1101:2394:1871#/1; ; +XXXXXXXXXX:7:1101:3387:100138#/1; ; +XXXXXXXXXX:7:1101:2269:1904#/1; ; +XXXXXXXXXX:7:1101:3444:100163#/1; ; +XXXXXXXXXX:7:1101:2259:1943#/1; ; +XXXXXXXXXX:7:1101:3371:100179#/1; ; +XXXXXXXXXX:7:1101:2371:1957#/1; ; +XXXXXXXXXX:7:1101:3311:100186#/1; ; +XXXXXXXXXX:7:1101:2394:1961#/1; ; +XXXXXXXXXX:7:1101:3438:100192#/1; ; +XXXXXXXXXX:7:1101:2333:1962#/1; ; +XXXXXXXXXX:7:1101:3479:100209#/1; ; +XXXXXXXXXX:7:1101:2459:1990#/1; ; +XXXXXXXXXX:7:1101:3417:100210#/1; ; +XXXXXXXXXX:7:1101:2372:1994#/1; ; +XXXXXXXXXX:7:1101:3452:100214#/1; ; +XXXXXXXXXX:7:1101:2677:1830#/1; ; +XXXXXXXXXX:7:1101:3354:100219#/1; ; +XXXXXXXXXX:7:1101:2603:1846#/1; ; +XXXXXXXXXX:7:1101:3600:100019#/1; ; +XXXXXXXXXX:7:1101:2535:1848#/1; ; diff -r 000000000000 -r fa3c3a64c993 test-data/taxonomy_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy_output.txt Wed Nov 24 21:52:14 2021 +0000 @@ -0,0 +1,100 @@ +XXXXXXXXXX:7:1101:1582:1835#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1610:1859#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1743:1871#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1536:1878#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2990:100153#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1624:1906#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1666:1926#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2921:100163#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1513:1929#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2759:100170#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1708:1937#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2981:100211#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1688:1946#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2767:100225#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1536:1959#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2797:100234#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1552:1976#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1748:1978#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2779:100239#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1593:1980#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2946:100242#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1987:1781#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3046:100006#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1900:1788#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3214:100027#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1848:1879#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3237:100032#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3027:100049#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1756:1891#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3238:100065#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1915:1901#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3198:100082#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1964:1931#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3088:100091#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1840:1948#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3105:100094#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1958:1952#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3190:100106#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1993:1999#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3117:100110#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2159:1798#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3147:100111#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2152:1838#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3065:100152#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2180:1843#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3154:100159#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2125:1861#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3198:100173#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2076:1911#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3166:100190#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2196:1920#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3225:100207#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2115:1927#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3019:100219#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2179:1937#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3202:100230#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2149:1945#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3211:100242#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2169:1964#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3168:100244#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3005:100246#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2313:1789#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3253:100014#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2361:1794#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2337:1794#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3284:100039#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2477:1795#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3310:100056#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2355:1821#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3420:100060#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2418:1834#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3267:100061#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2378:1838#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3416:100083#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2481:1853#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3411:100111#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3258:100128#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2252:1856#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3428:100129#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2394:1871#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3387:100138#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2269:1904#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3444:100163#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2259:1943#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3371:100179#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2371:1957#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3311:100186#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2394:1961#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3438:100192#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2333:1962#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3479:100209#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2459:1990#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3417:100210#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2372:1994#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3452:100214#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2677:1830#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3354:100219#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2603:1846#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3600:100019#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2535:1848#/1; ; No hits; 100;