diff RPKM_saturation.xml @ 50:f242ee103277 draft

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee

--- a/RPKM_saturation.xml	Thu Jul 16 17:43:43 2015 -0400
+++ b/RPKM_saturation.xml	Tue May 03 16:36:57 2016 -0400
@@ -77,17 +77,30 @@
         <data format="pdf" name="outputpdf" from_work_dir="output.saturation.pdf" label="${tool.name} on ${on_string} (PDF)"/>
     </outputs>
 
-    <!-- Unable to succefully run this script with test data
     <tests>
         <test>
-            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
-            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
-            <output name="outputxls" file="output.eRPKM.xls"/>
-            <output name="outputrawxls" file="output.rawCount.xls"/>
-            <output name="outputr" file="output.saturation.r"/>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
+            <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/>
+            <output name="outputxls">
+              <assert_contents>
+                <has_n_columns n="26" />
+                <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
+              </assert_contents>
+            </output>
+            <output name="outputrawxls">
+              <assert_contents>
+                <has_n_columns n="26" />
+                <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
+              </assert_contents>
+            </output>
+            <output name="outputr">
+              <assert_contents>
+                <has_text text="pdf('output.saturation.pdf')" />
+                <has_line_matching expression="S5=c\(\d+\.\d+\)" />
+              </assert_contents>
+            </output>
         </test>
     </tests>
-    -->
 
     <help><![CDATA[
 RPKM_saturation.py