<tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0">
	<description></description>
	<command interpreter="python">get_read.py $lib_file $map_file $output </command>
        <requirements>
                <requirement type="package" version="1.61">biopython</requirement>
                <requirement type="package" version="1.7.1">numpy</requirement>
                <requirement type="package" version="0.1.18">samtools</requirement>
        </requirements>
	<inputs>
                <param name="lib_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
		<param name="map_file" type="data" format="bam" label="Mapped file"/>
	</inputs>
	<outputs>
		<data name="output" format="txt"/>
	</outputs>
    <tests>
        <test>
            <param name="lib_file" value="test.bam" />
	        <param name="map_file" value="com_rna.txt" />
	        <output name="output" file="get_RT_stop_test.out" /> 
        </test>
    </tests>
	<help>


**TIPS**:

-----

**Input**

* 1. A mapped (bam) file from Bowtie (or any other mapping program)
* 2. Reference library sequences (fasta) used to map the reads to

-----

**Output**:

A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file)



	</help>
</tool>
