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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">
2 <description>Sorts the records in a FASTQ file based on the lexicographic ordering of their read names</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <version_command>fgbio --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[
9 fgbio SortFastq
10 --input '$input'
11 #if $input.is_of_type("fastq.gz", "fastqsanger.gz")
12 --output output.fastq.gz
13 && cp output.fastq.gz '$output'
14 #else
15 --output output.fastq
16 && cp output.fastq '$output'
17 #end if
18 ]]></command>
19 <inputs>
20 <param name="input" type="data" format="fastq,fastq.gz" label="fastq file to be sorted"/>
21 </inputs>
22 <outputs>
23 <data name="output" format_source="input" label="Sorted ${input.name}"/>
24 </outputs>
25 <help><![CDATA[
26 **fgbio SortFastq**
27
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.
29
30 http://fulcrumgenomics.github.io/fgbio/tools/latest/SortFastq.html
31 ]]></help>
32 <expand macro="citations" />
33 </tool>