Adjust test and add new one

pavanvidem · Jan 31, 2024 · 5752e8d · 5752e8d
1 parent 0f66b00
commit 5752e8d
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Showing 3 changed files with 1,709 additions and 3 deletions.
diff --git a/tools/htseq_count/htseq-count.xml b/tools/htseq_count/htseq-count.xml
@@ -180,6 +180,15 @@
             <output name="counts" file="htseq-test_counts.tsv" />
             <output name="allcounts" file="htseq-test_allcounts.tsv" />
         </test>
+        <test expect_num_outputs="2">
+            <!-- test SAM with no SQ lines and FASTA reference -->
+            <param name="samfile" value="htseq-test_nosq.sam" />
+            <param name="gfffile" value="htseq-test.gff" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="htseq-test_reference.fasta" />
+            <output name="counts" file="htseq-test_counts.tsv" />
+            <output name="allcounts" file="htseq-test_allcounts.tsv" />
+        </test>
         <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test.bam" />
             <param name="gfffile" value="htseq-test.gff" />
@@ -204,11 +213,9 @@
             <param name="gfffile" value="htseq-test.gff" />
             <param name="advanced_options_selector" value="advanced" />
             <param name="samout" value="true" />
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" value="htseq-test_reference.fasta" />
             <output name="counts" file="htseq-test_counts.tsv" />
             <output name="allcounts" file="htseq-test_allcounts.tsv" />
-            <output name="samoutfile" file="htseq-test_samout.bam" ftype="bam" compare="diff" lines_diff="6" />
+            <output name="samoutfile" file="htseq-test_samout.bam" ftype="bam" compare="diff" lines_diff="4" />
         </test>
         <test expect_num_outputs="2">
             <param name="samfile" value="htseq-test.sam" />