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

planemo upload commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

<?xml version="1.0" encoding="UTF-8"?>
<tool id="fasta2fastq" name="FASTA-to-FASTQ" version="1.0.0" profile="19.01">
    <description>Convert a FASTA file to a FASTQ file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command><![CDATA[
        python '$__tool_directory__/fasta2fastq.py' 
        -i '$file1'
        -o '$file2'
        -s '$score'
    ]]>
    </command>
    <inputs>
        <param name="file1" type="data" format="fasta" label="FASTA file" optional="false"/>
        <param name="score" type="integer" label="Quality score" value="40" help="Quality score for each base in all reads. Default = 40."/>
    </inputs>
    <outputs>
        <data name="file2" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
    </outputs>
    <tests>
        <test>
            <param name="file1" value="Reads_in.fasta"/>
            <output name="file2" file="Reads_out.fastq"/>
            <param name="score" value="40"/>
        </test>
    </tests>
    <help> <![CDATA[
**What it does**

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.

    ]]> 
    </help>
    <expand macro="citation" />
</tool>