<tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.4" profile="@PROFILE@">
    <description>tabulate descriptive stats for BAM datset</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

    <command><![CDATA[
    @ADDTHREADS@
    samtools flagstat -@ \$addthreads 
    #if $output_fmt != 'txt'
        --output-fmt $output_fmt
    #end if
    '$input1'
    > '$output1'
    ]]></command>

    <inputs>
        <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" />
        <param argument="--output-fmt" type="select" label="Output format">
            <option value="txt">txt</option>
            <option value="tsv">tsv</option>
            <option value="json">json</option>
        </param>
    </inputs>

    <outputs>
        <data name="output1" format="txt">
            <change_format>
                <when input="output_fmt" value="tsv" format="tabular" />
                <when input="output_fmt" value="json" format="json" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
            <output name="output1" file="samtools_flagstat_out1.txt" ftype="txt"/>
        </test>
        <test>
            <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
            <param name="output_fmt" value="tsv"/>
            <output name="output1" file="samtools_flagstat_out1.tsv" ftype="tabular" />
        </test>
        <test>
            <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
            <param name="output_fmt" value="json"/>
            <output name="output1" file="samtools_flagstat_out1.json" ftype="json" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::

  200 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  25 + 0 mapped (12.50%:nan%)
  200 + 0 paired in sequencing
  100 + 0 read1
  100 + 0 read2
  0 + 0 properly paired (0.00%:nan%)
  0 + 0 with itself and mate mapped
  25 + 0 singletons (12.50%:nan%)
  0 + 0 with mate mapped to a different chr
  0 + 0 with mate mapped to a different chr (mapQ>=5)

The results of samtools flagstat can be visualized with MultiQC.
    ]]></help>
    <expand macro="citations"/>
</tool>