<tool id="inner_distance" name="Inner Distance">
	<description>calculate the inner distance (or insert size) between two paired RNA reads</description>
	<requirements>
		<requirement type="package" version="2.15.1">R</requirement>
		<requirement type="package" version="2.3.7">rseqc</requirement>
	</requirements>
	<command interpreter="python"> inner_distance.py -i $input -o output -r $refgene

		#if $bounds.hasLowerBound
			-l $bounds.lowerBound
		#end if

		#if $bounds2.hasUpperBound
			-u $bounds2.upperBound
		#end if

		#if $steps.step
			-s $steps.stepSize
		#end if
	</command>
	<inputs>
		<param name="input" type="data" format="bam,sam" label="input bam/sam file" />
		<param name="refgene" type="data" format="bed" label="reference gene model" />
		<conditional name="bounds">
			<param name="hasLowerBound" type="boolean" label="Specify lower bound" value="false"/>
			<when value="true">
				<param name="lowerBound" type="integer" value="-250" label="Estimated Lower Bound (bp, default=-250)" />
			</when>
		</conditional>
		<conditional name="bounds2">
			<param name="hasUpperBound" type="boolean" label="Specify upper bound" value="false" />
			<when value="true">
				<param name="upperBound" type="integer" value="250" label="Estimated Upper Bound (bp, default=250)" />
			</when>
		</conditional>
		<conditional name="steps">
			<param name="step" type="boolean" label="Specify step size" value="false" />
			<when value="true">
				<param name="stepSize" type="integer" value="5" label="Step size (bp, default=5)" />
			</when>
		</conditional>
	</inputs>
	<outputs>
		<data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt"/>
		<data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" />
		<data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" />
		<data format="r" name="outputr" from_work_dir="output.inner_distance_plot.r" />
	</outputs>
	<help>
.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062

-----

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.

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

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

Reference gene model
	Gene model in BED format.

Estimated Upper/Lower Bounds (defaults=250 and -250)
	Estimated upper/lower bounds of inner distance (bp).

Step size (default=5)
	Step size of histogram


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

1. output.inner_distance.txt:
- first column is read ID
-second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start < Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1)
- third column indicates how paired reads were mapped: PE_within_same_exon, PE_within_diff_exon,PE_reads_overlap
2. output..inner_distance_freq.txt:
- inner distance starts
- inner distance ends
- number of read pairs
- note the first 2 columns are left side half open interval
3. output.inner_distance_plot.r: R script to generate histogram
4. output.inner_distance_plot.pdf: histogram plot

.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/inner_distance.png

	</help>
</tool>