changeset 36:846232fc30bf

Refactor normalize-by-median; use a virtualenv to install khmer

--- a/normalize-by-median.xml	Sun Jun 29 18:13:23 2014 -0400
+++ b/normalize-by-median.xml	Mon Jun 30 12:04:43 2014 -0400
@@ -21,13 +21,12 @@
 			--ksize=20
 			--n_tables=4
 			--min-tablesize=$parameters.tablesize
-			--cutoff=20
 		#else
 			--ksize=$parameters.ksize
 			--n_tables=$parameters.n_tables
 			--min-tablesize=$parameters.tablesize_specific
-			--cutoff=$parameters.cutoff
 		#end if
+		--cutoff=$cutoff
 		#if $save_countingtable
 			--savetable=$countingtable
 		#end if
@@ -60,12 +59,16 @@
 			type="boolean"
 			label="Save the k-mer counting table(s) in a file"
 			help="" />
-
+		<param	name="cutoff"
+			type="integer"
+			min="1"
+			value="20"
+			label="cutoff" />
 		<conditional name="parameters">
 			<param	name="type"
 				type="select"
 				label="Advanced Parameters"
-				help="ksize, n_tabless, a specific tablesize, cutoff" >
+				help="ksize, n_tables, a specific tablesize" >
 				<option	value="simple"
 					selected="true">
 					Hide
@@ -110,11 +113,6 @@
 					type="text"
 					label="tablesize"
 					help="lower bound on the tablesize to use" />
-				<param	name="cutoff"
-					type="integer"
-					min="1"
-					value="20"
-					label="cutoff" />
 			</when>
 		</conditional>
 	</inputs>
@@ -134,9 +132,12 @@
 	
 	<tests>
 		<test interactor="api">
-			<param name="inputs" value="test-abund-read-2.fa"/>
-			<param name="cutoff" value="1" />
-			<param name="ksize" value="17" />
+			<conditional name="parameters">
+				<param name="type" value="specific" />
+				<param name="inputs" value="test-abund-read-2.fa"/>
+				<param name="cutoff" value="1" />
+				<param name="ksize" value="17" />
+			</conditional>
 			<output name="output">
 				<discover_dataset name="test-abund-read-2.fa.keep">
 					<assert_contents>

--- a/tool_dependencies.xml	Sun Jun 29 18:13:23 2014 -0400
+++ b/tool_dependencies.xml	Mon Jun 30 12:04:43 2014 -0400
@@ -3,7 +3,7 @@
     <package name="khmer" version="1.1">
         <install version="1.0">
             <actions>
-                <action type="shell_command">easy_install -U setuptools==3.4.1; pip install --user khmer==1.1 || pip install khmer==1.1</action>
+		    <action type="setup_virtualenv">setuptools==3.4.1 khmer==1.1</action>
             </actions>
         </install>
     </package>