diff geneBody_coverage2.xml @ 59:dbedfc5f5a3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"

--- a/geneBody_coverage2.xml	Thu Nov 28 15:56:37 2019 -0500
+++ b/geneBody_coverage2.xml	Sat Dec 18 19:41:19 2021 +0000
@@ -1,8 +1,8 @@
-<tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@WRAPPER_VERSION@.1">
+<tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@.2">
     <description>
         Read coverage over gene body
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
@@ -21,6 +21,7 @@
     <inputs>
         <param name="input" type="data" label="Input bigwig file" format="bigwig" />
         <expand macro="refgene_param" />
+        <expand macro="rscript_output_param" />
     </inputs>
 
     <outputs>
@@ -30,12 +31,12 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" />
-            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
             <param name="rscript_output" value="true" />
             <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" />
-            <output name="outputr" file="output.geneBodyCoverage2.r" />
+            <output name="outputr" file="output.geneBodyCoverage2_r" />
             <output name="outputtxt" file="output.geneBodyCoverage2.txt" />
         </test>
     </tests>