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changeset 33:d067ee282412

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Switch line matching, api specification
author Michael R. Crusoe <mcrusoe@msu.edu>
date Sun, 29 Jun 2014 17:52:24 -0400
parents ceedaa33286e
children 7611b274ed67
files abundance-dist.xml count-median.xml filter-abund.xml normalize-by-median.xml
diffstat 4 files changed, 13 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/abundance-dist.xml	Sun Jun 29 17:35:17 2014 -0400
+++ b/abundance-dist.xml	Sun Jun 29 17:52:24 2014 -0400
@@ -44,8 +44,8 @@
 			<param name="no_zero" value="false" />
                     	<output name="output_histogram_filename">
 				<assert_contents>
-					<has_text text="1 96 96 0.98" />
-					<has_text text="1001 2 98 1.0" />
+					<has_line_matching expression="1 96 96 0.98" />
+					<has_line_matching expression="1001 2 98 1.0" />
 				</assert_contents>
 			</output>
 		</test>
@@ -55,8 +55,8 @@
  	                <param name="no_zero" value="false" />
                     	<output name="output_histogram_filename">
                             	<assert_contents>
-                                    	<has_text text="1 96 96 0.98" />
-                                    	<has_text text="255 2 98 1.0" />
+                                    	<has_line_matching="1 96 96 0.98" />
+                                    	<has_line_matching="255 2 98 1.0" />
                             	</assert_contents>
                     	</output>
             	</test>
--- a/count-median.xml	Sun Jun 29 17:35:17 2014 -0400
+++ b/count-median.xml	Sun Jun 29 17:52:24 2014 -0400
@@ -42,8 +42,8 @@
                         <param name="input_counting_table_filename" value="test-abund-read-2.ct" />
                         <output name="output_summary_filename">
                                 <assert_contents>
-                                        <has_text text="seq 1001 1001.0 0.0 18" />
-                                        <has_text text="895:1:37:17593:9954/1 1 103.803741455 303.702941895 114" />
+                                        <has_line_matching expression="seq 1001 1001.0 0.0 18" />
+                                        <has_line_matching expression="895:1:37:17593:9954/1 1 103.803741455 303.702941895 114" />
                                 </assert_contents>
                         </output>
 		</test>
--- a/filter-abund.xml	Sun Jun 29 17:35:17 2014 -0400
+++ b/filter-abund.xml	Sun Jun 29 17:52:24 2014 -0400
@@ -49,8 +49,8 @@
 		<exit_code	range="1:"
 				level="fatal" />
 	</stdio>
-        <tests interactor="api">
-                <test>
+        <tests>
+                <test interactor="api">
                         <param name="inputs" value="test-abund-read-2.fa" />
                         <param name="input_counting_table_filename" value="test-abund-read-2.ct" />
                         <output name="output">
@@ -61,7 +61,7 @@
 				</discover_dataset>
                         </output>
                 </test>
-                <test>
+                <test interactor="api">
                         <param name="input_sequence_filename" value="test-abund-read-2.fa" />
                         <param name="input_counting_table_filename" value="test-abund-read-2.ct" />
 			<param name="cutoff" value="1" />
--- a/normalize-by-median.xml	Sun Jun 29 17:35:17 2014 -0400
+++ b/normalize-by-median.xml	Sun Jun 29 17:52:24 2014 -0400
@@ -132,8 +132,8 @@
 				level="fatal" />
 	</stdio>
 	
-	<tests interactor="api">
-		<test>
+	<tests>
+		<test interactor="api">
 			<param name="inputs" value="test-abund-read-2.fa" />
 			<param name="cutoff" value="1" />
 			<param name="ksize" value="17" />
@@ -145,7 +145,7 @@
 				</discover_dataset>
 			</output>
 		</test>
-		<test>
+		<test interactor="api">
 			<param name="inputs" value="test-abund-read-2.fa" />
 			<param name="cutoff" value="2" />
 			<param name="ksize" value="17" />
@@ -158,7 +158,7 @@
 				</discover_dataset>
 			</output>
 		</test>
-		<test>
+		<test interactor="api">
 			<param name="inputs" value="test-abund-read-paired.fa" />
 			<param name="cutoff" value="1" />
 			<param name="ksize" value="17" />