<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@.1">
    <description>
     calculates the fragment size for each gene/transcript
    </description>

    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <expand macro="stdio" />

    <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command>

    <command><![CDATA[
        ln -sf '${input}' 'input.bam' &&
        ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
        RNA_fragment_size.py -i 'input.bam' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
        ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />
        <expand macro="refgene_param" />
        <expand macro="mapq_param" />
        <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)" />
    </inputs>

    <outputs>
        <data format="tabular" name="output" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
            <output name="output">
                <assert_contents>
                    <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" />
                    <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" />
                    <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" />
                    <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" />
                    <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" />
                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" />
                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" />
                    <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
RNA_fragment_size.py
++++++++++++++++++++

Calculate fragment size for each gene/transcript. For each transcript, it will
report : 1) Number of fragment that was used to estimate mean, median, std (see
below). 2) mean of fragment size 3) median of fragment size 4) stdev of fragment
size.

Inputs
++++++

Input BAM/SAM file
    Alignment file in BAM/SAM format.

Reference gene model
    Reference gene model in BED format. Must be strandard 12-column BED file.
    [required]

Minimum mapping quality
    Minimum mapping quality for an alignment to be considered as "uniquely
    mapped". default=30

Minimum number of fragments
    Minimum number of fragments. default=3

@ABOUT@

]]>

    </help>

    <expand macro="citations" />

</tool>