Mercurial > repos > galaxy-australia > hifiadapterfilt
changeset 1:41f5b4a4eac0 draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
| author | galaxy-australia |
|---|---|
| date | Wed, 14 Sep 2022 02:37:39 +0000 |
| parents | bbc2060caa0e |
| children | 03acc0e3772e |
| files | hifiadapterfilt.xml test-data/twistd.log |
| diffstat | 2 files changed, 22 insertions(+), 8 deletions(-) [+] |
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--- a/hifiadapterfilt.xml Mon Jul 11 03:09:58 2022 +0000 +++ b/hifiadapterfilt.xml Wed Sep 14 02:37:39 2022 +0000 @@ -2,7 +2,7 @@ <description>Remove CCS reads with remnant PacBio adapter sequences</description> <xrefs> <xref type='bio.tools'>hifiadapterfilt</xref> - </xrefs> + </xrefs> <macros> <import>macros.xml</import> </macros> @@ -68,7 +68,7 @@ **Input** -- input file - FASTQ and BAM. Also, gipped versions of FASTQ. +- input file - FASTQ and BAM. Also, gzipped versions of FASTQ. **Example:** @@ -77,21 +77,21 @@ **Output** - {prefix}.contaminant.blastout (Output of BLAST search) -- {prefix}.blocklist (Headers of PB adapter contaminated reads to be removed) -- {prefix}.filt.fastq.gz (Fastq reads free of PB adapter sequence ready for assembly) -- {prefix}.stats (File with simple math on number of reads removed, etc) +- {prefix}.blocklist (Headers of PacBio adapter contaminated reads to be removed) +- {prefix}.filt.fastq.gz (Fastq reads free of PacBio adapter sequence ready for assembly) +- {prefix}.stats (File with simple statistics for the number of reads removed, etc) .. class:: infomark **Contributor** -Galaxy Australia is the contributor wrapping the HiFiadapterFilt `Github <https://github.com/usegalaxy-au/tools-au>`_. - +Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this Github repository `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_. + **References** -More information are available on `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_. ]]></help> + <citations> <citation type="doi">DOI: 10.1186/s12864-022-08375-1</citation> </citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/twistd.log Wed Sep 14 02:37:39 2022 +0000 @@ -0,0 +1,14 @@ +2022-07-11T05:22:46+0000 [twisted.scripts._twistd_unix.UnixAppLogger#info] twistd 20.3.0 (/nfsmounts/qfab_data/bora_common/projects/10_380_Metagenomics_GVL_Matt_Field/venv_python3/bin/python 3.6.4) starting up. +2022-07-11T05:22:46+0000 [twisted.scripts._twistd_unix.UnixAppLogger#info] reactor class: twisted.internet.epollreactor.EPollReactor. +2022-07-11T05:22:46+0000 [-] Site starting on 8080 +2022-07-11T05:22:46+0000 [twisted.web.server.Site#info] Starting factory <twisted.web.server.Site object at 0x7f2ae20993c8> +2022-07-11T05:22:58+0000 [twisted.python.log#info] "118.208.94.230" - - [11/Jul/2022:05:22:58 +0000] "GET / HTTP/1.1" 200 1666 "-" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36" +2022-07-11T05:22:58+0000 [twisted.python.log#info] "118.208.94.230" - - [11/Jul/2022:05:22:58 +0000] "GET /favicon.ico HTTP/1.1" 404 145 "http://mike-sandpit.qfab.org:8080/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36" +2022-07-11T05:23:16+0000 [twisted.python.log#info] "45.113.233.251" - - [11/Jul/2022:05:23:15 +0000] "GET /combine.fastq.gz HTTP/1.1" 200 11009202 "-" "Python-urllib/3.8" +2022-07-11T05:23:58+0000 [twisted.web.http.HTTPChannel#info] Timing out client: IPv4Address(type='TCP', host='118.208.94.230', port=55436) +2022-07-11T05:23:58+0000 [twisted.web.http.HTTPChannel#info] Timing out client: IPv4Address(type='TCP', host='118.208.94.230', port=55435) +2022-07-11T05:24:08+0000 [-] Received SIGTERM, shutting down. +2022-07-11T05:24:08+0000 [-] (TCP Port 8080 Closed) +2022-07-11T05:24:08+0000 [twisted.web.server.Site#info] Stopping factory <twisted.web.server.Site object at 0x7f2ae20993c8> +2022-07-11T05:24:08+0000 [-] Main loop terminated. +2022-07-11T05:24:08+0000 [twisted.scripts._twistd_unix.UnixAppLogger#info] Server Shut Down.