Mercurial > repos > galaxy-australia > hifiadapterfilt

annotate 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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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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1 <tool id="hifiadapterfilt" name="HiFi Adapter Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" >
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2 <description>Remove CCS reads with remnant PacBio adapter sequences</description>
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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3 <xrefs>
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4 <xref type='bio.tools'>hifiadapterfilt</xref>
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41f5b4a4eac0 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
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5 </xrefs>
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <command><![CDATA[
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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13 @CLEAN_EXT@
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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15 #if $input_file.is_of_type("fastq.gz"):
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16 #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq.gz'
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17 #set prefix = $clean_ext($input_file.element_identifier)
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18 #elif $input_file.is_of_type("fastq"):
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19 #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq'
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20 #set prefix = $clean_ext($input_file.element_identifier)
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21 #elif $input_file.is_of_type("bam"):
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22 #set $inputfile = $clean_ext($input_file.element_identifier) + '.bam'
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23 #set prefix = $clean_ext($input_file.element_identifier)
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24 #end if
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25 ln -s '${input_file}' '${inputfile}' &&
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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27 bash pbadapterfilt.sh
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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28 -p '$prefix'
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29 -l '$match_length'
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30 -m '$match_percentage'
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31 -t\${GALAXY_SLOTS:-4}
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32 -o .
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33 && cp '$prefix'.filt.fastq.gz '$cleanfastq'
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34 && cp '$prefix'.contaminant.blastout '$blastout'
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35 && cp '$prefix'.blocklist '$blocklist'
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36 && cp '$prefix'.stats '$stats'
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37 ]]></command>
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38 <inputs>
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39 <param name="input_file" type="data" format="bam,fastq,fastq.gz" label="Input HiFi Reads" help="HiFi reads"/>
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40 <param argument="-l" name="match_length" type="integer" value="44" label="minimum length of adapter match to remove. Default=44" />
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41 <param argument="-m" name="match_percentage" type="integer" value="97" label="minimum percent Match of adapter to remove. Default=97" />
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42 </inputs>
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43 <outputs>
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44 <data name="cleanfastq" format="fastq.gz" label="${tool.name} on ${on_string}: clean reads"/>
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45 <data name="blastout" format="tabular" label="${tool.name} on ${on_string}: contaminant blastout"/>
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46 <data name="blocklist" format="txt" label="${tool.name} on ${on_string}: blocklist"/>
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47 <data name="stats" format="txt" label="${tool.name} on ${on_string}: contaminant statistic"/>
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48 </outputs>
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49
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50 <tests>
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51 <test>
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52 <!-- #1 test with common parameters -->
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53 <param name="input_file" value="combine.fastq.gz" ftype="fastq.gz"/>
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54 <param name="l" value="44" />
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55 <param name="m" value="97" />
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56 <output name="cleanfastq" file="combine.filt.fastq.gz" ftype="fastq.gz" decompress="true" />
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57 <output name="blastout" file="combine.contaminant.blastout" ftype="tabular" />
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58 <output name="blocklist" file="combine.blocklist" ftype="txt" />
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62
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63 .. class:: infomark
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64
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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65 **What it does**
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66
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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67 *Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences*
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68
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69 **Input**
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70
1
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71 - input file - FASTQ and BAM. Also, gzipped versions of FASTQ.
0
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72
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73 **Example:**
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74
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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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=. ]
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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76
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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77 **Output**
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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78
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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79 - {prefix}.contaminant.blastout (Output of BLAST search)
1
41f5b4a4eac0 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
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80 - {prefix}.blocklist (Headers of PacBio adapter contaminated reads to be removed)
41f5b4a4eac0 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
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81 - {prefix}.filt.fastq.gz (Fastq reads free of PacBio adapter sequence ready for assembly)
41f5b4a4eac0 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
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82 - {prefix}.stats (File with simple statistics for the number of reads removed, etc)
0
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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83
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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84
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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85 .. class:: infomark
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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86
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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87 **Contributor**
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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88
1
41f5b4a4eac0 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
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89 Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this Github repository `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_.
41f5b4a4eac0 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
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90
0
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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91 **References**
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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92
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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93 ]]></help>
1
41f5b4a4eac0 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 8b04bda034e2e05436e15c066fde316098714aa3"
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94
0
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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95 <citations>
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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96 <citation type="doi">DOI: 10.1186/s12864-022-08375-1</citation>
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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97 </citations>
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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98 </tool>