<macros>
    <token name="@TOOL_VERSION@">5.0.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@GALAXY_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">rseqc</xref>
        </xrefs>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
            <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
        </stdio>
    </xml>

    <!-- Params -->
    <xml name="bam_param">
        <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/>
    </xml>

    <xml name="bam_sam_param">
        <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/>
    </xml>

    <xml name="refgene_param">
        <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/>
    </xml>

    <xml name="mapq_param">
        <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" 
            help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot;"/>
    </xml>

    <xml name="readlength_param">
        <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/>
    </xml>

    <xml name="readnum_param">
        <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/>
    </xml>

    <xml name="sample_size_param">
        <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/>
    </xml>

    <xml name="min_intron_param">
        <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" />
    </xml>

    <xml name="layout_param">
        <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
            <option value="SE" selected="true">Single-end</option>
            <option value="PE">Paired-end</option>
        </param>
    </xml>

    <xml name="strand_type_param">
        <conditional name="strand_type">
            <param name="strand_specific" type="select" label="Strand-specific?">
                <option value="none" selected="true">None</option>
                <option value="pair">Pair-End RNA-seq</option>
                <option value="single">Single-End RNA-seq</option>
            </param>
            <when value="pair">
                <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)">
                    <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
                    <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
                </param>
            </when>
            <when value="single">
                <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)">
                    <option value="s" selected="true">positive --> positive; negative --> negative</option>
                    <option value="d">positive --> negative; negative --> positive</option>
                </param>
            </when>
            <when value="none"></when>
        </conditional>
    </xml>

    <xml name="multihits_param">
        <conditional name="multihits_type">
            <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)">
                <option value="use_multihits" selected="true">Count Mutliple Hit Reads</option>
                <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option>
            </param>
            <when value="skip_multihits">
                <expand macro="mapq_param" />
            </when>
            <when value="use_multihits" />
        </conditional>
    </xml>

    <xml name="rscript_output_param">
        <param name="rscript_output" type="boolean" value="false" label="Output R-Script"
            help="Output the R-Script used to generate the plots" />
    </xml>


    <!-- Output -->

    <xml name="pdf_output_data" token_filename="output.pdf">
        <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (pdf)" />
    </xml>

    <xml name="xls_output_data" token_filename="output.xls">
        <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (xls)" />
    </xml>

    <xml name="rscript_output_data" token_filename="output.r">
        <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (rscript)">
            <filter>rscript_output</filter>
        </data>
    </xml>

    <!-- Command -->
    <token name="@MULTIHITS@"><![CDATA[
        #if str($multihits_type.multihits_type_selector) == "skip_multihits"
            --skip-multi-hits
            --mapq=${multihits_type.mapq}
        #end if
    ]]></token>

    <token name="@BAM_SAM_INPUTS@"><![CDATA[
        #set $extension = str($input.ext)
        ln -s -f '${input}' 'input.${extension}' &&
        #if $extension == 'bam'
            ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' &&
        #end if
    ]]></token>

    <token name="@ABOUT@">

-----

About RSeQC
+++++++++++

The RSeQC_ package provides a number of useful modules that can comprehensively
evaluate high throughput sequence data especially RNA-seq data. "Basic modules"
quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC
bias, while "RNA-seq specific modules" investigate sequencing saturation status
of both splicing junction detection and expression estimation, mapped reads
clipping profile, mapped reads distribution, coverage uniformity over gene
body, reproducibility, strand specificity and splice junction annotation.

The RSeQC package is licensed under the GNU GPL v3 license.

.. image:: $PATH_TO_IMAGES/logo.png

.. _RSeQC: http://rseqc.sourceforge.net/


    </token>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts356</citation>
        </citations>
    </xml>
</macros>