# HG changeset patch
# User chrisd
# Date 1458678519 14400
# Node ID ce65eb39d17595dbaafe36d6a29e0cae8bb422ba
# Parent  2abae39582d30884e9296089b46ae6d462e0b633
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit cd089c5ccfa100bc4082861964f21c4d612dd49b

diff -r 2abae39582d3 -r ce65eb39d175 gene_fraction.xml
--- a/gene_fraction.xml	Wed Feb 24 14:27:51 2016 -0500
+++ b/gene_fraction.xml	Tue Mar 22 16:28:39 2016 -0400
@@ -25,7 +25,7 @@
 	<param name="max" type="integer" label="Ending sample level"
 	       value="1" min="1" max="100" help="(-max)" />
 	<param name="threshold" type="integer" label="Gene threshold"
-	       value="1" min="1" max="100" help="(-t)" />
+	       value="0" min="0" max="100" help="(-t)" />
 	<param name="skip" type="integer" label="Amount of levels to skip"
 	       value="1" min="1" max="100" help="(-skip)" />
 	<param name="samples" type="integer" label="Amount of samples per level"
@@ -42,16 +42,15 @@
       </test>
     </tests>
     <help><![CDATA[
-
 This program takes iterative samples from a SAM file with the goal of identifying the amount of a gene that is covered by a sample of reads.
         
-Program: Coverage Sampler 
-Contact: Chris Dean <cdean11@rams.colostate.edu
+Program: Coverage Sampler
+
+Contact: Chris Dean <cdean11@rams.colostate.edu>
 
 Usage: csa [options]
 
 Options:
-
     -amr_fp    amr database path
     -sam_fp    sam file path
     -min       starting level
@@ -59,10 +58,6 @@
     -skip      amount of levels to skip
     -t         gene fraction threshold
     -samples   amount of samples per level
-    -d         directory parsing
-    -bam       bam file parsing
     -out_fp    output file path
-
-
     ]]></help>
 </tool>
diff -r 2abae39582d3 -r ce65eb39d175 test-data/ref.fa
--- a/test-data/ref.fa	Wed Feb 24 14:27:51 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->seq1
-AAAAA
diff -r 2abae39582d3 -r ce65eb39d175 test-data/result.txt
diff -r 2abae39582d3 -r ce65eb39d175 test-data/test.sam