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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit a786695a05177842dcc89ef6bb21b38d7e7ce2db"
author iuc
date Wed, 06 Oct 2021 12:04:36 +0000
parents 7a82006f7c05
children 372def2f8fd6
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5ceeb5a5d70f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit a786695a05177842dcc89ef6bb21b38d7e7ce2db"
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1 <tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy1" 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 #for $i, $elem in enumerate($input)
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13 ln -fs '$elem' inputs/fastq${i}.fastq &&
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14 #end for
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15 artic guppyplex --min-length $min_length --max-length $max_length
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16 --directory inputs/
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17 --prefix artic_guppyplex --output '$output1'
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="input" multiple="true" type="data" format="fastq" label="Nanopore reads (FASTQ format" />
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22 <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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23 <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" />
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24 <param name="skip_quality_check" argument="--skip-quality-check" type="boolean" truevalue="--skip-quality-check" falsevalue="" checked="False" label="Do not filter on quality score (speeds up processing)" />
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25 </inputs>
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26 <outputs>
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27 <data name="output1" format="fastq" from_work_dir="run_name_.fastq" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input" value="test.fastq" />
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32 <output name="output1" file="gupplyplex_output.fastq"/>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 The ARTIC_ guppyplex tool filters reads by length and (optionally) quality.
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37 This filter is typically used as a pre-processing step in the processing
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38 of amplicon sequencing Nanopore reads, where a size-based filter can
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39 be used to remove possibly-chimeric reads.
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40
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41 The default paramters of the tool (minimum length of 400 and maximum of 700)
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42 are based on the ARTIC amplicon scheme. If used with a different amplicon
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43 scheme they should be adjusted to use the minimum length of an amplicon as
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44 the minimum length and the maximum length of an amplicon plus 200 as the
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45 maximum length.
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46
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47 .. _ARTIC: https://artic.readthedocs.io/en/latest/
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48 ]]></help>
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49 <expand macro="citations" />
1
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50 </tool>