# HG changeset patch
# User bgruening
# Date 1411148591 14400
# Node ID 59845dc3331f1c92bb069e304565840600b8b498
# Parent  6ed004769284b4b0ff74921174e725d09859ff6f
Uploaded

diff -r 6ed004769284 -r 59845dc3331f macs2_bdgbroadcall.xml
--- a/macs2_bdgbroadcall.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_bdgbroadcall.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -55,4 +55,5 @@
 
 @citation@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_bdgcmp.xml
--- a/macs2_bdgcmp.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_bdgcmp.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -77,4 +77,5 @@
 
 @citation@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_bdgdiff.xml
--- a/macs2_bdgdiff.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_bdgdiff.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -80,4 +80,5 @@
 
 @citation@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_bdgpeakcall.xml
--- a/macs2_bdgpeakcall.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_bdgpeakcall.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -56,4 +56,5 @@
 
 @citation@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_callpeak.xml
--- a/macs2_callpeak.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_callpeak.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -35,16 +35,11 @@
         ## advanced options
         #if $advanced_options.advanced_options_selector == 'on':
             $advanced_options.nolambda
-            $advanced_options.call_summits
             #if $advanced_options.broad_options.broad_options_selector == 'broad':
                 --broad
                 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
-            #end if
-
-            #if $advanced_options.keepdup.keepdup_opt == 'specific':
-                --keep-dup '${ $advanced_options.keepdup.keep_duplicates }'
-            #else
-                --keep-dup '${ $advanced_options.keepdup.keepdup_opt }'
+            #else:
+                $advanced_options.broad_options.call_summits
             #end if
 
             #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
@@ -91,15 +86,15 @@
         #end if
 
         #if 'html' in str($outputs).split(','):
-            ## if output files exists, move them to the extra_files_path and create a html result page linking to them
+            ## if output files exists, move them to the files_path and create a html result page linking to them
             &amp;&amp;
             (
             count=`ls -1 MACS2* 2>/dev/null | wc -l`;
             if [ \$count != 0 ];
             then 
-                mkdir "${ output_extra_files.extra_files_path }";
-                cp MACS2* "${ output_extra_files.extra_files_path }";
-                python "\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.extra_files_path }" $temp_stderr > "${ output_extra_files }";
+                mkdir "${ output_extra_files.files_path }";
+                cp MACS2* "${ output_extra_files.files_path }";
+                python "\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.files_path }" $temp_stderr > "${ output_extra_files }";
             fi;
             )
         #end if
@@ -196,7 +191,7 @@
         <data name="output_bed" format="bed" label="${tool.name} on ${on_string} (Peaks in BED format)">
             <filter>'peaks_bed' in outputs</filter>
         </data>
-        <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
+        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_broad_peaks.bed" label="${tool.name} on ${on_string} (broad Peaks)">
             <filter>
             ((
               advanced_options['advanced_options_selector'] == "on" and
@@ -280,4 +275,5 @@
 
 @citation@
   </help>
+  <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_filterdup.xml
--- a/macs2_filterdup.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_filterdup.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -8,7 +8,7 @@
     <command>
         macs2 filterdup
             -i "${ infile }"
-            -o "${ outfile }"
+            -o temp_outfile
 
         --format '${ infile.extension.upper() }'
         @effective_genome_size@
@@ -19,6 +19,8 @@
         #else
             --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
         #end if
+	;
+	mv temp_outfile "${ outfile }"
     </command>
     <expand macro="stdio" />
     <inputs>
@@ -50,4 +52,5 @@
 
 @citation@
   </help>
+  <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_macros.xml
--- a/macs2_macros.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_macros.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -89,4 +89,9 @@
 
 Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
     </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/gb-2008-9-9-r137</citation>
+        </citations>
+    </xml>
 </macros>
diff -r 6ed004769284 -r 59845dc3331f macs2_predictd.xml
--- a/macs2_predictd.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_predictd.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -66,4 +66,5 @@
 
 @citation@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_randsample.xml
--- a/macs2_randsample.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_randsample.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -50,4 +50,5 @@
 
 @citation@
   </help>
+  <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f macs2_refinepeak.xml
--- a/macs2_refinepeak.xml	Wed May 21 15:34:41 2014 -0400
+++ b/macs2_refinepeak.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -41,4 +41,5 @@
 
 @citation@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 6ed004769284 -r 59845dc3331f tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 21 15:34:41 2014 -0400
+++ b/tool_dependencies.xml	Fri Sep 19 13:43:11 2014 -0400
@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="numpy" version="1.7.1">
-       <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="84125ffacb90" 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="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="a983dc7c8103" 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="1c0e86a44f73" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1c0e86a44f73" name="package_r_3_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="gnu_awk" version="4.1.0">
-       <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_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>
@@ -27,10 +27,10 @@
                 <action type="shell_command">git submodule update --recursive</action>
 
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.7.1" />
                     </repository>
-                    <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>