# HG changeset patch
# User chrisd
# Date 1467267350 14400
# Node ID ec439b0e7512c3437887aa99d598560d69f4b50a
# Parent  fa1aae53a2f38f63f4880c48bb4f083af17690f8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 9982b8cd32dc6ecef17cd8c3bf16f42d8eb30d75-dirty

diff -r fa1aae53a2f3 -r ec439b0e7512 coverage_sampler.xml
--- a/coverage_sampler.xml	Tue Jun 28 23:31:46 2016 -0400
+++ b/coverage_sampler.xml	Thu Jun 30 02:15:50 2016 -0400
@@ -1,7 +1,7 @@
 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
     <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description>
     <requirements>
-	<requirement type="package" version="0.1">csa</requirement>
+	<requirement type="package" version="0.1">coverage_sampler</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -57,24 +57,48 @@
       </test>
     </tests>
     <help><![CDATA[
-A simple tool for calculating the amount of a gene that is covered by a sample of alignments.
+
+**Coverage sampler**
 
-Program: Coverage Sampler
+Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes
+in as input a fasta and alignment file. The output of this program is a tab delimited text file describing the fraction of each gene
+that was covered from a random sampling of alignments.
+
+------
 
-Contact: Chris Dean <cdean11@rams.colostate.edu>
+**Options**
+
+    -min     INT    Starting level to sample reads from (level is in percent)
+
+    -max     INT    Ending level to sample reads from (level is in percent)
 
-Usage: csa [options]
+    -skip    INT    Number of levels to skip
+
+    -samples  INT    Number of iterations per sample level
+
+    -t       INT    Gene fraction threshold (only genes with a gene fraction greater than this threshold are output)
 
-Options:
-    -ref_fp    STR/FILE	    	ref file path
-    -sam_fp    STR/FILE	    	sam file path
-    -min       INT      		starting sample level
-    -max       INT	        	ending sample level
-    -skip      INT	        	amount of sample levels to skip
-    -t         INT	        	gene fraction threshold
-    -samples   INT	        	iterations per sample level
-    -out_fp    STR/FILE	    	output file path
-    ]]></help>
+------
+
+**Output**
+
+A tab delimited text file with the following columns::
+
+    Level		The sampling level alignments were taken at
+    Iteration		The iteration number of the current sample level
+    Gene Id		The reference name having a gene fraction greater than threshold
+    Gene Fraction	The gene fraction for the current reference sequence (in percent)
+    Hits		The number of alignments associated with the reference sequence
+
+------
+
+**Development**
+
+Development is being done on github_
+
+.. _github: https://github.com/cdeanj/coverage_sampler
+
+ ]]></help>
     <citations>
     </citations>
 </tool>
diff -r fa1aae53a2f3 -r ec439b0e7512 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 28 23:31:46 2016 -0400
+++ b/tool_dependencies.xml	Thu Jun 30 02:15:50 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="csa" version="0.1">
+    <package name="coverage_sampler" version="0.1">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/cdeanj/coverage_sampler.git</action>