annotate artic_guppyplex.xml @ 3:00e20a06ff1e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41716a0929d9eb829e0772016ae9c24f24cf4b7e
author iuc
date Wed, 21 Jun 2023 15:45:22 +0000
parents 372def2f8fd6
children
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1 <tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy2" profile="20.09">
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2 <description>Filter Nanopore reads by read length and (optionally) quality</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 mkdir inputs &&
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12
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13 ## Note about compression handling in the following:
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14 ## guppyplex use mimetypes.guess_type to guess compression so
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15 ## it's important to get the suffix of the inputs right.
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16 ## Even if it detects compressed input, it will write uncompressed
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17 ## output so we need to handle output compression separately.
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18
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19 ## symlink input files to appropriate names in the inputs/ directory
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20 bash prepare_inputs.sh &&
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21 #if str($input.structure) == 'one_to_one':
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22 #set $compressed = $input.reads.is_of_type("fastq.gz", "fastqsanger.gz")
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23 #else:
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24 #set $compressed = next(iter($input.reads)).is_of_type("fastq.gz", "fastqsanger.gz")
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25 #end if
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26 artic guppyplex --min-length $min_length --max-length $max_length
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27 #if $min_quality == 0:
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28 --skip-quality-check
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29 #else:
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30 --quality $min_quality
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31 #end if
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32 --directory inputs/
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33 --output guppyplex_out.fastq
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34 #if $compressed:
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35 && gzip guppyplex_out.fastq
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36 #end if
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37 ]]>
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38 </command>
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39 <configfiles>
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40 <configfile filename="prepare_inputs.sh"><![CDATA[
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41 #if str($input.structure) == 'one_to_one':
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42 ln -s '$input.reads' inputs/1.${input.reads.ext}
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43 #else:
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44 #for $i, $elem in enumerate($input.reads):
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45 ln -s '$elem' inputs/${i}.${elem.ext} &&
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46 #end for
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47 :
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48 #end if
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49 ]]>
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50 </configfile>
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51 </configfiles>
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52 <inputs>
2
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53 <conditional name="input">
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54 <param name="structure" type="select"
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55 label="Structure of your input data"
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56 help="">
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57 <option value="one_to_one">One input dataset per sample</option>
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58 <option value="one_to_many">Multiple input datasets per sample</option>
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59 </param>
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60 <when value="one_to_one">
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61 <param name="reads" type="data" format="@FASTQ_FORMATS@"
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62 label="Sequencing dataset(s) - one per sample" />
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63 </when>
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64 <when value="one_to_many">
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65 <param name="reads" multiple="true" type="data" format="@FASTQ_FORMATS@"
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66 label="Partial sequencing datasets for your sample"
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67 help="Multiple datasets selected here will get combined into a single output for a single assumed sample. Select a nested list to have its inner lists interpreted as data from one sample each and to obtain one output per inner list." />
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68 </when>
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69 </conditional>
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70 <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" />
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71 <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" />
2
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72 <param name="min_quality" type="integer" min="0" value="7"
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73 label="Eliminate reads with a mean base quality score of less than"
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74 help="Set to 0 to skip the quality check." />
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75 </inputs>
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76 <outputs>
2
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77 <data name="output" format_source="reads" from_work_dir="guppyplex_out.fastq*" />
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78 </outputs>
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79 <tests>
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80 <test>
2
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81 <conditional name="input">
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82 <param name="structure" value="one_to_one" />
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83 <param name="reads" value="test.fastq" />
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84 </conditional>
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85 <output name="output" file="gupplyplex_output.fastq"/>
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86 </test>
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87 <test>
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88 <conditional name="input">
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89 <param name="structure" value="one_to_many" />
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90 <param name="reads" value="test.fastq,test.fastq" />
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91 </conditional>
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92 <!-- guppyplex drops duplicate reads so we don't need a new
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93 test file for checking this branch -->
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94 <output name="output" file="gupplyplex_output.fastq"/>
0
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98 The ARTIC_ guppyplex tool filters reads by length and (optionally) quality.
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99 This filter is typically used as a pre-processing step in the processing
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100 of amplicon sequencing Nanopore reads, where a size-based filter can
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101 be used to remove possibly-chimeric reads.
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102
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103 The default paramters of the tool (minimum length of 400 and maximum of 700)
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104 are based on the ARTIC amplicon scheme. If used with a different amplicon
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105 scheme they should be adjusted to use the minimum length of an amplicon as
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106 the minimum length and the maximum length of an amplicon plus 200 as the
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107 maximum length.
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108
2
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109 The tool can also be used simultaneously to gather partial fastq
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110 datasets into single datasets per sample.
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111
0
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112 .. _ARTIC: https://artic.readthedocs.io/en/latest/
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113 ]]></help>
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114 <expand macro="citations" />
1
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115 </tool>