# HG changeset patch
# User galaxy-australia
# Date 1663123059 0
# Node ID 41f5b4a4eac092a6b977df63006da39512f09563
# Parent  bbc2060caa0e4a1cdd95fc03beb3d1836554bd2c
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"

diff -r bbc2060caa0e -r 41f5b4a4eac0 hifiadapterfilt.xml
--- 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>
diff -r bbc2060caa0e -r 41f5b4a4eac0 test-data/twistd.log
--- /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.