# HG changeset patch
# User iuc
# Date 1444663182 14400
# Node ID 37f53bf6c2b104fb945b51221ed8b8096fc71c7f
# Parent  d188dfa05d71f7578b1a1762acfe7d835e085010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74

diff -r d188dfa05d71 -r 37f53bf6c2b1 macs2_callpeak.xml
--- 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**
diff -r d188dfa05d71 -r 37f53bf6c2b1 macs2_macros.xml
--- a/macs2_macros.xml	Mon Jun 01 23:00:45 2015 -0400
+++ b/macs2_macros.xml	Mon Oct 12 11:19:42 2015 -0400
@@ -27,7 +27,7 @@
             <when value="121400000" />
             <when value="93260000" />
             <when value="user_defined">
-                <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/>
+                <param name="gsize" type="integer" label="Effective genome size" value=""/>
             </when>
         </conditional>
     </xml>
diff -r d188dfa05d71 -r 37f53bf6c2b1 test-data/magic.pdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/magic.pdf	Mon Oct 12 11:19:42 2015 -0400
@@ -0,0 +1,1 @@
+%PDF-1.4
diff -r d188dfa05d71 -r 37f53bf6c2b1 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jun 01 23:00:45 2015 -0400
+++ b/tool_dependencies.xml	Mon Oct 12 11:19:42 2015 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="numpy" version="1.7.1">
-       <repository changeset_revision="bbfe29f56566" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="5c489d2d630b" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-       <repository changeset_revision="0d5ee829daaa" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="63808602082c" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="R_3_0_1" version="3.0.1">
         <repository changeset_revision="e5c96827ef85" name="package_r_3_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -13,7 +13,7 @@
        <repository changeset_revision="440a5170003f" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="macs2" version="2.1.0">
-       <repository changeset_revision="aa9a6f914bd5" name="package_macs2_2_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="88853ce35531" name="package_macs2_2_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>