Mercurial > repos > iuc > artic_guppyplex

annotate artic_guppyplex.xml @ 6:cb137e439d5d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 9fe39fd1ad0c1a5af9e8d2d633fd3e7404adbac7
author iuc
date Mon, 24 Feb 2025 13:54:25 +0000
parents 301e84974e34
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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301e84974e34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
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1 <tool id="artic_guppyplex" name="ARTIC guppyplex" version="@TOOL_VERSION@+galaxy0" 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 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 mkdir inputs &&
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11 ## Note about compression handling in the following:
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12 ## guppyplex use mimetypes.guess_type to guess compression so
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13 ## it's important to get the suffix of the inputs right.
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14 ## Even if it detects compressed input, it will write uncompressed
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15 ## output so we need to handle output compression separately.
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17 ## symlink input files to appropriate names in the inputs/ directory
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18 bash prepare_inputs.sh &&
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19 #if str($input.structure) == 'one_to_one':
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20 #set $compressed = $input.reads.is_of_type("fastq.gz", "fastqsanger.gz")
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21 #else:
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22 #set $compressed = next(iter($input.reads)).is_of_type("fastq.gz", "fastqsanger.gz")
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23 #end if
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25 artic guppyplex
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26 --min-length $min_length
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27 --max-length $max_length
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28 #if $min_quality == 0:
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29 --skip-quality-check
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30 #else:
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31 --quality $min_quality
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32 #end if
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33 --directory inputs/
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34 --output guppyplex_out.fastq
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35 #if $compressed:
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36 && gzip guppyplex_out.fastq
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37 #end if
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38 ]]>
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39 </command>
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40 <configfiles>
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41 <configfile filename="prepare_inputs.sh"><![CDATA[
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42 #if str($input.structure) == 'one_to_one':
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43 ln -s '$input.reads' inputs/1.${input.reads.ext}
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44 #else:
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45 #for $i, $elem in enumerate($input.reads):
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46 ln -s '$elem' inputs/${i}.${elem.ext} &&
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47 #end for
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48 :
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49 #end if
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50 ]]>
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51 </configfile>
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52 </configfiles>
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53 <inputs>
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54 <conditional name="input">
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55 <param name="structure" type="select"
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56 label="Structure of your input data"
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57 help="">
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58 <option value="one_to_one">One input dataset per sample</option>
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59 <option value="one_to_many">Multiple input datasets per sample</option>
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60 </param>
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61 <when value="one_to_one">
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62 <param name="reads" type="data" format="@FASTQ_FORMATS@"
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63 label="Sequencing dataset(s) - one per sample" />
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64 </when>
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65 <when value="one_to_many">
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66 <param name="reads" multiple="true" type="data" format="@FASTQ_FORMATS@"
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67 label="Partial sequencing datasets for your sample"
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68 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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69 </when>
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70 </conditional>
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71 <param name="max_length" type="integer" value="700" min="1" label="Maximum read length" help="Remove reads greater than this number of base pairs" />
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72 <param name="min_length" type="integer" value="400" min="1" label="Minimum read length" help="Remove reads less than this number of base pairs" />
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73 <param name="min_quality"
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74 optional="true" type="integer" min="0" value="7"
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75 label="Minimum read quality"
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76 help="Remove reads with average quality lower than this number. Set to 0 to skip the quality check." />
0
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77 </inputs>
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78 <outputs>
3
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79 <data name="output" format_source="reads" from_work_dir="guppyplex_out.fastq*" />
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80 </outputs>
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81 <tests>
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82 <test>
3
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83 <conditional name="input">
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84 <param name="structure" value="one_to_one" />
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85 <param name="reads" value="test.fastq.gz" />
3
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86 </conditional>
5
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87 <output name="output">
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88 <assert_contents>
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89 <has_size value="72300" delta="1000" />
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90 </assert_contents>
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91 </output>
3
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92 </test>
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93 <test>
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94 <conditional name="input">
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95 <param name="structure" value="one_to_many" />
5
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96 <param name="reads" value="test.fastq.gz,test.fastq.gz" />
3
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97 </conditional>
5
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98 <output name="output">
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99 <assert_contents>
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100 <has_size value="72300" delta="200" />
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101 </assert_contents>
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102 </output>
0
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106 The ARTIC_ guppyplex tool filters reads by length and (optionally) quality.
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107 This filter is typically used as a pre-processing step in the processing
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108 of amplicon sequencing Nanopore reads, where a size-based filter can
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109 be used to remove possibly-chimeric reads.
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110
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111 The default paramters of the tool (minimum length of 400 and maximum of 700)
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112 are based on the ARTIC amplicon scheme. If used with a different amplicon
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113 scheme they should be adjusted to use the minimum length of an amplicon as
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114 the minimum length and the maximum length of an amplicon plus 200 as the
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115 maximum length.
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116
3
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117 The tool can also be used simultaneously to gather partial fastq
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118 datasets into single datasets per sample.
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119
0
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120 .. _ARTIC: https://artic.readthedocs.io/en/latest/
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121 ]]></help>
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122 <expand macro="citations" />
2
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123 </tool>