# HG changeset patch
# User Michael R. Crusoe <mcrusoe@msu.edu>
# Date 1404157031 14400
# Node ID 0f23e940217265edef12fb48d88d258376a9d976
# Parent  1727dd6f7374e252eb7694030d57c96e6be3b6ad
Include countingtable output for a-d-s

diff -r 1727dd6f7374 -r 0f23e9402172 abundance-dist-single.xml
--- a/abundance-dist-single.xml	Mon Jun 30 12:20:45 2014 -0400
+++ b/abundance-dist-single.xml	Mon Jun 30 15:37:11 2014 -0400
@@ -21,10 +21,11 @@
 $zero
 $bigcount
 #if $save_countingtable
---savetable=$countingtable_to_save
+--savetable=$optional_output_countingtable
 #end if
 --report-total-kmers
 --squash
+@THREADS@
 $input_sequence_filename
 $output_histogram_filename	
 	</command>
@@ -45,6 +46,11 @@
 		<expand macro="tableinputs" />
 	</inputs>
 	<outputs>
+		<data	name="optional_output_countingtable"
+			format="ct"
+			label="${tool.name} k-mer counting table from #echo ', '.join(map(str, $inputs)))#">
+			<filter>save_countingtable == True</filter>
+		</data>
 		<expand macro="abundance-histogram-output" />	
 	</outputs>
  	<stdio>
diff -r 1727dd6f7374 -r 0f23e9402172 filter-abund.xml
--- a/filter-abund.xml	Mon Jun 30 12:20:45 2014 -0400
+++ b/filter-abund.xml	Mon Jun 30 15:37:11 2014 -0400
@@ -19,6 +19,7 @@
   --cutoff=$cutoff
 #fi
 $variable_coverage
+@THREADS@
 $countingtable_to_load
 #for input in $inputs
  $input
@@ -74,7 +75,7 @@
                         </output>
                 </test>
         </tests> 
-	<!-- [OPTIONAL] Help displayed in Galaxy -->
+	<!-- [OPTIONAL] ReST Help displayed in Galaxy -->
     <!--
 	<help>
 	</help>
diff -r 1727dd6f7374 -r 0f23e9402172 macros.xml
--- a/macros.xml	Mon Jun 30 12:20:45 2014 -0400
+++ b/macros.xml	Mon Jun 30 15:37:11 2014 -0400
@@ -14,7 +14,8 @@
   --ksize=$parameters.ksize
   --n_tables=$parameters.n_tables
   --min-tablesize=$parameters.tablesize_specific
-#end if</token>
+  #end if</token>
+	<token name="@THREADS@">--threads \$GALAXY_SLOTS</token>
 	<xml name="tableinputs">
 		<conditional name="parameters">
 			<param	name="type"