Mercurial > repos > rnateam > chipseeker

diff chipseeker.xml @ 5:4c2dbe4dbb4e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
author: rnateam
date: Tue, 04 Dec 2018 10:01:20 -0500
parents: 90fe78a19b55
children: b418a1d3585d
--- a/chipseeker.xml	Mon Nov 26 06:21:37 2018 -0500
+++ b/chipseeker.xml	Tue Dec 04 10:01:20 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="chipseeker" name="ChIPseeker" version="1.16.1">
+<tool id="chipseeker" name="ChIPseeker" version="1.16.2">
     <description>for ChIP peak annotation and visualization</description>
     <requirements>
         <requirement type="package" version="1.16.1">bioconductor-chipseeker</requirement>
@@ -30,7 +30,9 @@
             -D $adv.flankgenedist
         #end if
         -f $format
-        -p $pdf
+        #if $pdf:
+            -p $pdf
+        #end if
         -r $rdata
     ]]>
     </command>
@@ -142,6 +144,13 @@
             <output name="out_tab" ftype="tabular" file="outflank.tab" />
             <output name="out_plots" file="out.pdf" compare="sim_size"/>
         </test>
+        <!-- Ensure the tool works when no plots are outputed -->
+        <test expect_num_outputs="1">
+            <param name="peaks" value="in.interval" ftype="interval"/>
+            <param name="gtf_source_select" value="cached"/>
+            <param name="pdf" value=""/>
+            <output name="out_tab" ftype="interval" file="outint.int" />
+        </test>
     </tests>
     <help><![CDATA[