view ubu_sam2fastq.xml @ 0:aa2cf6718319 draft default tip

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<tool id="ubu_sam2fastq" name="UBU sam2fastq" version="0.1.0">
    <description>Convert a SAM/BAM file to FASTQ</description>

    <requirements>
        <requirement version="1.2">ubu</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command><![CDATA[
        java -Xmx1G -jar \$UBU_JAR sam2fastq --in $input --fastq1 paired1.fastq --fastq2 paired2.fastq --end1 '$end1' --end2 '$end2'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="sam,bam" label="Sam or Bam file to convert" />
        <param name="end1" type="text" value="/1" label="Id suffix used to identify the first read in a pair." />
        <param name="end2" type="text" value="/2" label="Id suffix used to identify the second read in a pair." />
    </inputs>
    <outputs>
        <data name="fastq1" format="data" from_work_dir="paired1.fastq" />
        <data name="fastq2" format="data" from_work_dir="paired2.fastq" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="sam2fastq_test.sam" />
            <output name="fastq1" file="sam2fastq_expected_paired1.fastq"/>
            <output name="fastq2" file="sam2fastq_expected_paired2.fastq"/>
        </test>
    </tests>
    <help><![CDATA[
        input SAM/BAM file
Option                                  Description                            
------                                  -----------                            
--in                                    Required input sam or bam file         
--fastq1                                Required output FASTQ file             
--fastq2                                Second FASTQ file for paired end       
--end1                                  Id suffix used to identify the first   
                                          read in a pair.  i.e. /1 (omit this  
                                          option to use bit flag)              
--end2                                  Id suffix used to identify the second  
                                          read in a pair.  i.e. /2 (omit this  
                                          option to use bit flag)              

    ]]></help>
</tool>