# HG changeset patch
# User nml
# Date 1477340591 14400
# Node ID c0c9883788388c994b028cf5e9f62c718a8f7b0a
# Parent  4263967e8d402eb37d5a42758f97a9b987050c94
planemo upload commit 6bde05f38465311441e89cfa070f03d3b6edad1b

diff -r 4263967e8d40 -r c0c988378838 first
--- a/first	Tue May 17 15:56:30 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-1
\ No newline at end of file
diff -r 4263967e8d40 -r c0c988378838 merge.xml
--- a/merge.xml	Tue May 17 15:56:30 2016 -0400
+++ b/merge.xml	Mon Oct 24 16:23:11 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="collapse_dataset" name="Collapse Collection" version="2.1">
+<tool id="collapse_dataset" name="Collapse Collection" version="3.0">
   <description>Collapse collection into single dataset in order of the collection</description>
   <command>
     <![CDATA[
@@ -6,13 +6,17 @@
      (
     #for $f in $input_list#
     #if $filename.add_name:
-       #if str($filename.place_name) ==  "same":
-           printf "$f.element_identifier\t" ;
-       #else
-           printf "$f.element_identifier\n" ;
+       #if str($filename.place_name) ==  "same_once":
+           printf "$f.element_identifier\t"; cat "$f";
+       #elif str($filename.place_name) ==  "same_multiple":
+           awk '{print "$f.element_identifier\t"$0}' "$f";
+       #elif str($filename.place_name) ==  "above":
+           printf "$f.element_identifier\n"; cat "$f";
        #end if
+    #else:
+       cat "$f" ;
     #end if
-    cat "$f" ;
+
     #end for#
     )
     > $output
@@ -21,12 +25,13 @@
     
   </command>
   <inputs>
-     <param name="input_list" type="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" />
+     <param name="input_list" type="data" format="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" />
      <conditional name="filename">
      <param name="add_name" type="boolean" display="checkboxes" label="Append File name"/>
      <when value="true">
        <param name="place_name" type="select" label="Where to add dataset name">
-         <option value="same">Same line</option>
+         <option value="same_once">Same line and only once per dataset</option>
+         <option value="same_multiple">Same line and each line in dataset</option>
          <option value="above">Line Above</option>
        </param>
      </when>
@@ -38,20 +43,18 @@
     <data name="output" format_source="input_list" ></data>
   </outputs>
   <tests>
-	<test>
-	        <param name="input_list">
-        	  <collection type="list">
-	            <element name="input1" value="input1" />
-        	    <element name="input2" value="input2" />
-	          </collection>
-		</param>
-		<output name="output" file="answer.txt"/>
-	</test>
+    <test>
+      <param name="input_list">
+        <collection type="list">
+	  <element name="input1" value="input1" />
+          <element name="input2" value="input2" />
+	</collection>
+      </param>
+      <output name="output" file="answer.txt"/>
+    </test>
   </tests>
   <help>
 	Combines a list collection into a single file dataset with option to include dataset names.
-        
-        
   </help>
   <citations>
   </citations>
diff -r 4263967e8d40 -r c0c988378838 second
--- a/second	Tue May 17 15:56:30 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-2
\ No newline at end of file
diff -r 4263967e8d40 -r c0c988378838 third
--- a/third	Tue May 17 15:56:30 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-3
\ No newline at end of file