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"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
author jjohnson
date Thu, 19 Aug 2021 15:13:55 +0000
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1 <tool id="fgbio_sort_fastq" name="fgbio SortFastq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>Sorts the records in a FASTQ file based on the lexicographic ordering of their read names</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 <version_command>fgbio --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 fgbio SortFastq
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10 --input '$input'
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11 #if $input.is_of_type("fastq.gz", "fastqsanger.gz")
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12 --output output.fastq.gz
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13 && cp output.fastq.gz '$output'
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14 #else
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15 --output output.fastq
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16 && cp output.fastq '$output'
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <param name="input" type="data" format="fastq,fastq.gz" label="fastq file to be sorted"/>
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21 </inputs>
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22 <outputs>
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23 <data name="output" format_source="input" label="Sorted ${input.name}"/>
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24 </outputs>
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25 <help><![CDATA[
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26 **fgbio SortFastq**
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27
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28 Sorts a FASTQ file. Sorts the records in a FASTQ file based on the lexicographic ordering of their read names. Input and output files can be either uncompressed or gzip-compressed.
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29
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30 http://fulcrumgenomics.github.io/fgbio/tools/latest/SortFastq.html
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31 ]]></help>
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32 <expand macro="citations" />
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33 </tool>