annotate fasta2fastq.xml @ 0:8ab09593f2eb draft default tip

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author mheinzl
date Wed, 07 Oct 2020 18:48:40 +0000
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="fasta2fastq" name="FASTA-to-FASTQ" version="1.0.0" profile="19.01">
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3 <description>Convert a FASTA file to a FASTQ file</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <command><![CDATA[
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8 python '$__tool_directory__/fasta2fastq.py'
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9 -i '$file1'
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10 -o '$file2'
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11 -s '$score'
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="file1" type="data" format="fasta" label="FASTA file" optional="false"/>
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16 <param name="score" type="integer" label="Quality score" value="40" help="Quality score for each base in all reads. Default = 40."/>
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17 </inputs>
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18 <outputs>
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19 <data name="file2" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="file1" value="Reads_in.fasta"/>
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24 <output name="file2" file="Reads_out.fastq"/>
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25 <param name="score" value="40"/>
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26 </test>
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27 </tests>
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28 <help> <![CDATA[
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29 **What it does**
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30
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31 Takes a FASTA file and converts it to a FASTQ file by adding a static quality score. The default quality score for each base in all reads is 40.
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32
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33 ]]>
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34 </help>
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35 <expand macro="citation" />
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36 </tool>