diff macs2_callpeak.xml @ 4:56e104999978 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e

--- a/macs2_callpeak.xml	Wed Jan 27 15:23:25 2016 -0500
+++ b/macs2_callpeak.xml	Mon Feb 06 02:30:37 2017 -0500
@@ -66,8 +66,6 @@
             #if str($cutoff_options.pvalue).strip() != '':
                 --pvalue "${ cutoff_options.pvalue }"
             #end if
-        #else:
-            --foldenrichment "${ cutoff_options.foldenrichment }"
         #end if
 
         ## model options
@@ -121,7 +119,6 @@
             <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
                 <option value="qvalue" selected="true">q-value</option>
                 <option value="pvalue">p-value</option>
-                <option value="foldenrichment">foldenrichment</option>
             </param>
             <when value="pvalue">
                 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection"
@@ -131,10 +128,6 @@
                 <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection"
                     help="default: 0.05 (--qvalue)"/>
             </when>
-            <when value="foldenrichment">
-                <param name="foldenrichment" value="" type="integer" label="Foldenrichment cutoff for peak detection"
-                    help="(--foldenrichment)"/>
-            </when>
         </conditional>
 
         <conditional name="nomodel_type">
@@ -150,14 +143,13 @@
             </when>
         </conditional>
 
-        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build">
+        <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" label="Outputs" help="PDF only created when model is build">
             <option value="peaks_tabular" selected="True">Peaks as tabular file</option>
             <!--<option value="narrow">narrow Peaks</option>-->
             <option value="summits" selected="true">summits</option>
             <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
             <option value="html">Summary page (html)</option>
             <option value="pdf">Plot in PDF</option>
-            <validator type="no_options" message="Please select at least one output file." />
         </param>
 
         <conditional name="advanced_options">