# HG changeset patch
# User fastaptamer
# Date 1421280405 18000
# Node ID b54808c59f87711f700dcbc04cb18a2d986aaaba

Uploaded

diff -r 000000000000 -r b54808c59f87 fastaptamer_enrich_1.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastaptamer_enrich_1.xml	Wed Jan 14 19:06:45 2015 -0500
@@ -0,0 +1,58 @@
+<tool id="fastaptamer_enrich_1_0_1" name="FASTAptamer-Enrich" version="1.0.1">
+
+	<description>Calculate fold-enrichment of each sequence across populations</description>
+	
+	<version_command>fastaptamer_enrich -v</version_command>
+	
+	<command interpreter="perl">fastaptamer_enrich -x $input_x -y $input_y -o $output -f $filter
+		# if str(input_z) != ''
+			-z "${input_z}"
+		# end if
+	</command>
+	
+	<inputs>
+		<param name="input_x" type="data" format="fasta" label="Input file X"  help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
+		<param name="input_y" type="data" format="fasta" label="Input file Y"  help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
+		<param name="input_z" type="data" format="fasta" optional="true"  label="Input file Z"  help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
+		<param name="filter" type="float" optional="true" value="0"  label="RPM Threshold Filter" help="Sequences with an aggregate RPM (across all populations) less than supplied value will be excluded from analysis"></param>
+ 	</inputs>
+ 	
+    <outputs>
+    	<data name="output" format="tabular" label="FASTAptamer-Enrich output file"></data>
+ 	</outputs>
+
+    <help>
+
+.. class:: warningmark
+
+FASTAptamer-Enrich requires FASTA formatted input files generated by FASTAptamer-Count or FASTAptamer-Cluster.
+
+------
+
+**FASTAptamer-Enrich** rapidly calculates "fold-enrichment" values for each sequence across two or three input files.  Output is provided as a tab-delimited file and is formatted to include sequence composition, length, rank, reads, reads per million (RPM), cluster information (if available) and enrichment values for each sequence. 
+
+An optional threshold filter can be applied to exclude sequences with total reads per million (across all input populations) less than the number supplied.
+
+Enrichment is calculated by dividing reads per million of y/x (and z/y and z/x, if a third input file is specified).
+
+------
+
+.. 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.2015.7X</citation>
+    </citations>
+	
+</tool>