diff get_reads/get_read.xml~ @ 25:90bc1ead3abd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reads/get_read.xml~	Mon Oct 20 14:41:41 2014 -0400
@@ -0,0 +1,43 @@
+<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="0.1.18">samtools</requirement>
+        </requirements>
+	<inputs>
+                <param name="lib_file" type="data" format="fasta" label="Library file (fasta)"/>
+		<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 mapping program)
+2. Reference library sequences (fasta) used to map the reads
+
+-----
+
+**Output**:
+A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file)	
+
+
+
+	</help>
+</tool>