I do not think this is a good idea

it takes so much time on something with marginal benefits.
pavanvidem · Sep 20, 2023 · f131de5 · f131de5
1 parent ddbfc74
commit f131de5
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/tools/trinity/abundance_estimates_to_matrix.xml b/tools/trinity/abundance_estimates_to_matrix.xml
@@ -89,7 +89,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
             <param name="est_method" value="RSEM"/>
             <param name="cross_sample_norm" value="TMM"/>
@@ -112,7 +112,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/>
             <param name="est_method" value="RSEM"/>
             <param name="cross_sample_norm" value="TMM"/>
@@ -135,7 +135,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/>
             <param name="est_method" value="eXpress"/>
             <param name="cross_sample_norm" value="TMM"/>
@@ -158,7 +158,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
             <param name="est_method" value="RSEM"/>
             <param name="cross_sample_norm" value="UpperQuartile"/>
@@ -180,7 +180,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
             <param name="est_method" value="RSEM"/>
             <param name="cross_sample_norm" value="none"/>
@@ -197,7 +197,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/>
             <param name="est_method" value="salmon"/>
             <param name="cross_sample_norm" value="none"/>
@@ -214,7 +214,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/>
             <param name="est_method" value="kallisto"/>
             <param name="cross_sample_norm" value="TMM"/>

diff --git a/tools/trinity/align_and_estimate_abundance.xml b/tools/trinity/align_and_estimate_abundance.xml
@@ -180,7 +180,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="paired_or_single" value="paired"/>
             <param name="left_input" value="reads.left.fq.gz"/>
             <param name="right_input" value="reads.right.fq.gz"/>
@@ -203,7 +203,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="paired_or_single" value="paired"/>
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
@@ -226,7 +226,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="paired_or_single" value="paired"/>
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
@@ -249,7 +249,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="paired_or_single" value="paired"/>
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>

diff --git a/tools/trinity/analyze_diff_expr.xml b/tools/trinity/analyze_diff_expr.xml
@@ -96,7 +96,7 @@
     </outputs>
     <tests>
         <!-- Test without GO enrichment analysis -->
-        <test>
+        <test expect_num_outputs="9">
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
             <param name="samples" value="count/samples.txt"/>
             <param name="DE_results">
@@ -125,7 +125,7 @@
             <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
         </test>
         <!-- Test without GO enrichment analysis, test name of DE_results input files different from those generated by tool run_de_analysis.pl -->
-        <test>
+        <test expect_num_outputs="9">
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
             <param name="samples" value="count/samples.txt"/>
             <param name="DE_results">
@@ -154,7 +154,7 @@
             <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
         </test>
         <!-- Test with GO enrichment analysis -->
-        <test>
+        <test expect_num_outputs="10">
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
             <param name="samples" value="count/samples.txt"/>
             <param name="DE_results">