# HG changeset patch
# User fastaptamer
# Date 1423596159 18000
# Node ID 2bed8ca187a1b7ae457d14d76ee1eb968346659e

Uploaded

diff -r 000000000000 -r 2bed8ca187a1 fastaptamer_count_1.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastaptamer_count_1.xml	Tue Feb 10 14:22:39 2015 -0500
@@ -0,0 +1,59 @@
+<tool id="fastaptamer_count_1_0_2" name="FASTAptamer-Count" version="1.0.2">
+
+	<description>Count, rank, sort and normalize sequence reads in a selection population.</description>
+	
+	<version_command>fastaptamer_count -v</version_command>
+	
+	<command interpreter="perl">fastaptamer_count -i $input -o $output</command>
+
+	<inputs>
+		<param name="input" type="data" format="fastq" label="Input file"  help="Must be FASTQ and should be pre-processed (filtered for quality and trimmed of constant regions)."></param>
+ 	</inputs>
+ 	
+    <outputs>
+    	<data name="output" format="fasta" label="FASTAptamer-Count output file"></data>
+ 	</outputs>
+    
+    <help>
+
+.. class:: warningmark
+
+FASTAptamer-Count requires FASTQ formatted input files.
+
+.. class:: infomark
+
+Input files should be trimmed of constant regions and filtered for only high-quality reads.
+
+------
+
+**FASTAptamer-Count** serves as the gateway to the FASTAptamer suite of bioinformatics tools for combinatorial selections.  
+
+For a given FASTQ input file, FASTAptamer-Count will determine the number of times each sequence was read, normalize sequence frequency to reads per million, and rank and sort sequences by decreasing total reads.
+
+Output is generated as a sorted and non-redundant FASTA formatted file in which each unique sequence generates a FASTA entry with the following information in the description line:
+
+	>RANK-READS-RPM
+
+RANK is the relative abundance of the sequence within the population. In cases where two or more sequences are sampled with equal abundance, FASTAptamer-Count follows standard competition ranking (e.g., “1-2-2-4” where two sequences are tied for second).  READS is the raw number of times a sequence was counted. RPM is “Reads per million,” which is a normalized value that allows for comparison across populations of varying read depth. RPM is calculated as: RPM = (READS/(population size)) x 10^6.
+
+------
+
+.. image:: 
+	http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png
+	:height: 98
+	:width: 300
+
+For more information on FASTAptamer, visit our website_.
+
+FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_.
+
+.. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt
+.. _website: http://burkelab.missouri.edu/fastaptamer.html
+
+    </help>
+
+    <citations>
+    	<citation type="doi">doi:10.1038/mtna.2015.4</citation>
+    </citations>
+    
+</tool>