<tool id="rseqc_read_GC" name="Read GC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>determines GC% and read count</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        read_GC.py
            --input-file 'input.${extension}'
            --out-prefix output
            --mapq ${mapq}
        ]]>
    </command>

    <inputs>
        <expand macro="bam_sam_param" />
        <expand macro="mapq_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
        <expand macro="xls_output_data" filename="output.GC.xls" label="${tool.name} on ${on_string}: XLS"/>
        <expand macro="rscript_output_data" filename="output.GC_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="rscript_output" value="true" />
            <output name="outputxls" file="output.GC.xls" />
            <output name="outputr" file="output.GC_plot_r" />
            <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" />
        </test>
    </tests>

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


Inputs
++++++++++++++

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

Output
++++++++++++++

1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
2. output.GC_plot.r: R script to generate pdf file.
3. output.GC_plot.pdf: graphical output generated from R script.

.. image:: $PATH_TO_IMAGES/read_gc.png
   :height: 600 px
   :width: 600 px
   :scale: 80 %

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>