Mercurial > repos > galaxy-australia > hifiadapterfilt

comparison hifiadapterfilt.xml @ 1:41f5b4a4eac0 draft

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"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
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0:bbc2060caa0e 1:41f5b4a4eac0
1 <tool id="hifiadapterfilt" name="HiFi Adapter Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" > 1 <tool id="hifiadapterfilt" name="HiFi Adapter Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" >
2 <description>Remove CCS reads with remnant PacBio adapter sequences</description> 2 <description>Remove CCS reads with remnant PacBio adapter sequences</description>
3 <xrefs> 3 <xrefs>
4 <xref type='bio.tools'>hifiadapterfilt</xref> 4 <xref type='bio.tools'>hifiadapterfilt</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
66 66
67 *Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences* 67 *Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences*
68 68
69 **Input** 69 **Input**
70 70
71 - input file - FASTQ and BAM. Also, gipped versions of FASTQ. 71 - input file - FASTQ and BAM. Also, gzipped versions of FASTQ.
72 72
73 **Example:** 73 **Example:**
74 74
75 - bash pbadapterfilt.sh [ -p file Prefix ] [ -l minimum Length of adapter match to remove. Default=44 ] [ -m minimum percent Match of adapter to remove. Default=97 ] [ -t Number of threads for blastn. Default=8 ] [ -o outdirectory prefix Default=. ] 75 - bash pbadapterfilt.sh [ -p file Prefix ] [ -l minimum Length of adapter match to remove. Default=44 ] [ -m minimum percent Match of adapter to remove. Default=97 ] [ -t Number of threads for blastn. Default=8 ] [ -o outdirectory prefix Default=. ]
76 76
77 **Output** 77 **Output**
78 78
79 - {prefix}.contaminant.blastout (Output of BLAST search) 79 - {prefix}.contaminant.blastout (Output of BLAST search)
80 - {prefix}.blocklist (Headers of PB adapter contaminated reads to be removed) 80 - {prefix}.blocklist (Headers of PacBio adapter contaminated reads to be removed)
81 - {prefix}.filt.fastq.gz (Fastq reads free of PB adapter sequence ready for assembly) 81 - {prefix}.filt.fastq.gz (Fastq reads free of PacBio adapter sequence ready for assembly)
82 - {prefix}.stats (File with simple math on number of reads removed, etc) 82 - {prefix}.stats (File with simple statistics for the number of reads removed, etc)
83 83
84 84
85 .. class:: infomark 85 .. class:: infomark
86 86
87 **Contributor** 87 **Contributor**
88 88
89 Galaxy Australia is the contributor wrapping the HiFiadapterFilt `Github <https://github.com/usegalaxy-au/tools-au>`_. 89 Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this Github repository `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_.
90 90
91 **References** 91 **References**
92 92
93 More information are available on `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_.
94 ]]></help> 93 ]]></help>
94
95 <citations> 95 <citations>
96 <citation type="doi">DOI: 10.1186/s12864-022-08375-1</citation> 96 <citation type="doi">DOI: 10.1186/s12864-022-08375-1</citation>
97 </citations> 97 </citations>
98 </tool> 98 </tool>