Mercurial > repos > galaxy-australia > hifiadapterfilt
changeset 0:bbc2060caa0e draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
author | galaxy-australia |
---|---|
date | Mon, 11 Jul 2022 03:09:58 +0000 |
parents | |
children | 41f5b4a4eac0 |
files | README.md hifiadapterfilt.xml macros.xml test-data/combine.blocklist test-data/combine.contaminant.blastout test-data/combine.fastq.gz test-data/combine.filt.fastq.gz |
diffstat | 7 files changed, 4345 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Jul 11 03:09:58 2022 +0000 @@ -0,0 +1,21 @@ +# HiFiAdapterFilt +Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz). + +# Dependencies +- BamTools +- BLAST+ + +# Installation +Currently only tested on Ubuntu + +# Docker +- HiFiAdapterFilt Docker is available on https://hub.docker.com/r/dmolik/pbadapterfilt + +``` +docker pull dmolik/pbadapterfilt +docker run -t -d -v /hifireads_data_directory_on_host_machine/:/home/genomics/HiFiAdapterFilt-master/ubuntu --name hifiadapterfilt dmolik/pbadapterfilt +docker exec -it <container_id> /bin/bash + +``` + +See [official documentation](https://github.com/sheinasim/HiFiAdapterFilt) for more details.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hifiadapterfilt.xml Mon Jul 11 03:09:58 2022 +0000 @@ -0,0 +1,98 @@ +<tool id="hifiadapterfilt" name="HiFi Adapter Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" > + <description>Remove CCS reads with remnant PacBio adapter sequences</description> + <xrefs> + <xref type='bio.tools'>hifiadapterfilt</xref> + </xrefs> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command><![CDATA[ + + @CLEAN_EXT@ + + #if $input_file.is_of_type("fastq.gz"): + #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq.gz' + #set prefix = $clean_ext($input_file.element_identifier) + #elif $input_file.is_of_type("fastq"): + #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq' + #set prefix = $clean_ext($input_file.element_identifier) + #elif $input_file.is_of_type("bam"): + #set $inputfile = $clean_ext($input_file.element_identifier) + '.bam' + #set prefix = $clean_ext($input_file.element_identifier) + #end if + ln -s '${input_file}' '${inputfile}' && + + bash pbadapterfilt.sh + -p '$prefix' + -l '$match_length' + -m '$match_percentage' + -t\${GALAXY_SLOTS:-4} + -o . + && cp '$prefix'.filt.fastq.gz '$cleanfastq' + && cp '$prefix'.contaminant.blastout '$blastout' + && cp '$prefix'.blocklist '$blocklist' + && cp '$prefix'.stats '$stats' + ]]></command> + <inputs> + <param name="input_file" type="data" format="bam,fastq,fastq.gz" label="Input HiFi Reads" help="HiFi reads"/> + <param argument="-l" name="match_length" type="integer" value="44" label="minimum length of adapter match to remove. Default=44" /> + <param argument="-m" name="match_percentage" type="integer" value="97" label="minimum percent Match of adapter to remove. Default=97" /> + </inputs> + <outputs> + <data name="cleanfastq" format="fastq.gz" label="${tool.name} on ${on_string}: clean reads"/> + <data name="blastout" format="tabular" label="${tool.name} on ${on_string}: contaminant blastout"/> + <data name="blocklist" format="txt" label="${tool.name} on ${on_string}: blocklist"/> + <data name="stats" format="txt" label="${tool.name} on ${on_string}: contaminant statistic"/> + </outputs> + + <tests> + <test> + <!-- #1 test with common parameters --> + <param name="input_file" value="combine.fastq.gz" ftype="fastq.gz"/> + <param name="l" value="44" /> + <param name="m" value="97" /> + <output name="cleanfastq" file="combine.filt.fastq.gz" ftype="fastq.gz" decompress="true" /> + <output name="blastout" file="combine.contaminant.blastout" ftype="tabular" /> + <output name="blocklist" file="combine.blocklist" ftype="txt" /> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +*Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences* + +**Input** + +- input file - FASTQ and BAM. Also, gipped versions of FASTQ. + +**Example:** + +- 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=. ] + +**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) + + +.. class:: infomark + +**Contributor** + +Galaxy Australia is the contributor wrapping the HiFiadapterFilt `Github <https://github.com/usegalaxy-au/tools-au>`_. + +**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> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 11 03:09:58 2022 +0000 @@ -0,0 +1,29 @@ +<macros> + <token name="@TOOL_VERSION@">2.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <token name="@DIGEST@">99b5e479baee5ffe01c676dd3d7180b0d3eb94af08db0f2ceb3641bef3ebbaa4</token> + <xml name="requirements"> + <requirements> + <container type="docker">dmolik/pbadapterfilt:latest</container> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@CLEAN_EXT@"> + <![CDATA[ + #from os.path import splitext + #import re + #def clean_ext($identifier) + #while $identifier.endswith(('.fq','.fastq', '.fastq.gz','.bam')) + #set $identifier = splitext($identifier)[0] + #end while +$identifier#slurp + #end def + ]]> + </token> +</macros>
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