# HG changeset patch
# User iuc
# Date 1517429533 18000
# Node ID f0b351e734b8b705882ed831c2a0ad4244431acf
# Parent  acbd3fb47f90a778e53840538a061045da373713
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e9415c8ba21c77f848a57d60ee6be78dff4b49a6

diff -r acbd3fb47f90 -r f0b351e734b8 macs2_callpeak.xml
--- a/macs2_callpeak.xml	Thu Jan 25 02:11:52 2018 -0500
+++ b/macs2_callpeak.xml	Wed Jan 31 15:12:13 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.2">
+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3">
     <description>Call peaks from alignment results</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -102,7 +102,7 @@
         #end if
 
         ## run R to create pdf from model script
-        #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(','):
+        #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE":
             &&
             Rscript MACS2_model.r > MACS2_model.r.log
         #end if
@@ -206,7 +206,7 @@
             <option value="summits">Peak summits</option>
             <option value="bdg" >Scores in bedGraph files (--bdg)</option>
             <option value="html">Summary page (html)</option>
-            <option value="pdf">Plot in PDF</option>
+            <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
         </param>
 
         <section name="advanced_options" title="Advanced Options">
@@ -274,7 +274,8 @@
             <filter>
             ((
               outputs and 'pdf' in outputs and
-              nomodel_type['nomodel_type_selector'] == "create_model"
+              nomodel_type['nomodel_type_selector'] == "create_model" and
+              format != "BAMPE"
             ))
             </filter>
         </data>
@@ -335,6 +336,8 @@
             <param name="gsize" value="3300000000"/>
             <param name="nomodel_type_selector" value="nomodel"/>
             <param name="nolambda" value="True"/>
+            <!-- we select PDF as output, but since we are in BAMPE mode, this will not ignored and the expect_num_outputs stays one. -->
+            <param name="outputs" value="pdf"/>
             <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
         </test>
     </tests>