# HG changeset patch
# User iuc
# Date 1525009977 14400
# Node ID 4dd515072667a72b7b662408ae62de28f76b17f9
# Parent  d8c5761a8ba7817771fa1eca014330b1bf9909a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df

diff -r d8c5761a8ba7 -r 4dd515072667 htseq-count.xml
--- a/htseq-count.xml	Mon Feb 05 15:04:17 2018 -0500
+++ b/htseq-count.xml	Sun Apr 29 09:52:57 2018 -0400
@@ -158,43 +158,43 @@
             </actions>
         </data>
         <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
-            <filter>samout_conditional['samout'] == "Yes"</filter>
+            <filter>advanced_options['advanced_options_selector'] == 'advanced' and  advanced_options['samout_conditional']['samout'] == "Yes"</filter>
         </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test.sam" />
             <param name="gfffile" value="htseq-test.gff" />
             <output name="counts" file="htseq-test_counts.tsv" />
             <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test.sam" />
             <param name="gfffile" value="htseq-test.gff" />
             <output name="counts" file="htseq-test_counts.tsv" />
             <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test.bam" />
             <param name="gfffile" value="htseq-test.gff" />
             <output name="counts" file="htseq-test_counts.tsv" />
             <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test-paired.bam" />
             <param name="gfffile" value="htseq-test.gff" />
             <output name="counts" file="htseq-test-paired_counts.tsv" />
             <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test-paired.bam" />
             <param name="gfffile" value="htseq-test.gff" />
             <param name="samout" value="No" />
             <output name="counts" file="htseq-test-paired_counts.tsv" />
             <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="samfile" value="htseq-test.sam" />
             <param name="gfffile" value="htseq-test.gff" />
             <param name="advanced_options_selector" value="advanced" />
@@ -205,7 +205,7 @@
             <output name="othercounts" file="htseq-test_othercounts.tsv" />
             <output name="samoutfile" file="htseq-test_samout.bam" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test.sam" />
             <param name="gfffile" value="htseq-test.gff" />
             <param name="advanced_options_selector" value="advanced" />