# HG changeset patch
# User tyty
# Date 1419015506 18000
# Node ID 40b8071a44f7318d41c8859f0fe7da5334c14152
# Parent  5a9183ec344f135214761b022e96c83fb9b8983c
Deleted selected files

diff -r 5a9183ec344f -r 40b8071a44f7 get_reads/get_read.xml
--- a/get_reads/get_read.xml	Fri Dec 19 13:23:03 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<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**
-
-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>