diff RNA_fragment_size.xml @ 54:5873cd7afb67 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82

--- a/RNA_fragment_size.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/RNA_fragment_size.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@">
+<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@.1">
     <description>
      calculates the fragment size for each gene/transcript
     </description>
@@ -35,7 +35,18 @@
         <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="output" file="output.RNA_fragment_size.txt" />
+            <output name="output">
+                <assert_contents>
+                    <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" />
+                    <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" />
+                    <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" />
+                </assert_contents>
+            </output>
         </test>
     </tests>