changeset 89:361dc1047dc0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reads/get_read.xml	Fri Dec 19 13:58:50 2014 -0500
@@ -0,0 +1,46 @@
+<tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0">
+	<description>derives the reverse transcriptase (RT) stop count on each nucleotide from a mapped file provided by the Iterative Mapping module</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>
+
+
+**Function**
+
+Get RT Stop Counts derives the RT stop counts on each nucleotide of each transcript in the reference transcriptome based on a mapped file (.bam), typically the output from the Iterative Mapping module.
+
+-----
+
+**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>