diff macs2_callpeak.xml @ 44:37f53bf6c2b1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74

--- a/macs2_callpeak.xml	Mon Jun 01 23:00:45 2015 -0400
+++ b/macs2_callpeak.xml	Mon Oct 12 11:19:42 2015 -0400
@@ -85,7 +85,7 @@
         #end if
 
         ## run R to create pdf from model script
-        #if 'pdf' in str($outputs).split(','):
+        #if $nomodel_type.nomodel_type_selector == 'create_model' and 'pdf' in str($outputs).split(','):
             &&
             Rscript MACS2_model.r > MACS2_model.r.log
         #end if
@@ -151,7 +151,7 @@
             </when>
         </conditional>
 
-        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
+        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build">
             <option value="peaks_bed" selected="True">Peaks as BED file</option>
             <!--<option value="narrow">narrow Peaks</option>-->
             <option value="summits" selected="true">summits</option>
@@ -235,7 +235,12 @@
             <filter>'summits' in outputs</filter>
         </data>
         <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
-            <filter>'pdf' in outputs</filter>
+            <filter>
+            ((
+              'pdf' in outputs and
+              nomodel_type['nomodel_type_selector'] == "create_model"
+            ))
+            </filter>
         </data>
         <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
             <filter>'bdg' in outputs</filter>
@@ -262,6 +267,17 @@
             <output name="output_bed" compare="contains" file="callpeak_part.bed"/>
             <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/>
         </test>
+        <test>
+            <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
+            <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
+            <param name="cutoff_options_selector" value="qvalue"/>
+            <param name="qvalue" value="0.05"/>
+            <param name="band_width" value="300"/>
+            <param name="outputs" value="pdf"/>
+            <param name="effective_genome_size_options_selector" value="user_defined" />
+            <param name="gsize" value="3300000000" />
+            <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" />
+        </test>
     </tests>
     <help>
 **What it does**