--- a/multijoin.xml	Sun Oct 06 08:22:36 2013 -0400
+++ b/multijoin.xml	Wed Jan 07 11:10:52 2015 -0500
@@ -1,49 +1,64 @@
-<tool id="tp_multijoin'_tool" name="Multi-Join" version="0.1.1">
-  <description>(combine multiple files)</description>
-  <command interpreter="perl">multijoin
+<tool id="tp_multijoin'_tool" name="Multi-Join" version="@BASE_VERSION@.0">
+    <description>(combine multiple files)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="5.18">perl</requirement>
+        <requirement type="package" version="1.0">text_processing_perl_packages</requirement>
+    </expand>
+    <command interpreter="perl">
+<![CDATA[
+    multijoin
         --key '$key_column'
         --values '$value_columns'
         --filler '$filler'
         $ignore_dups
         $output_header
         $input_header
-        $first_filename
-        #for $file in $files
-            '$file.filename'
+        $first_file
+        #for $file in $files:
+            '$file'
         #end for
-        &gt; '$output'
-  </command>
+        > '$outfile'
+]]>
+    </command>
+    <inputs>
+        <param name="first_file" type="data" format="txt" label="File to join"/>
+        <param name="files" multiple="True" type="data" format="txt" label="add additional file" />
 
-  <inputs>
+        <param name="key_column" label="Common key column" type="integer"
+            value="1" help="Usually gene-ID or other common value" />
 
-    <param name="first_filename" label="File to join" type="data" format="txt" />
-    <repeat name="files" title="with" min="2">
-        <param name="filename" label="add additional file" type="data" format="txt" />
-    </repeat>
-
-    <param name="key_column" label="Common key column" type="integer"
-       value="1" help="Usually gene-ID or other common value" />
+        <param name="value_columns" label="Column with values to preserve" 
+            type="data_column" data_ref="first_file" accept_default="true" multiple="True" display="checkboxes"/>
 
-    <param name="value_columns" label="Column with values to preserve" 
-        type="data_column" data_ref="first_filename" accept_default="true" multiple="True" display="checkboxes"/>
-
-    <param name="output_header" type="boolean" checked="false" truevalue="--out-header" falsevalue="" label="Add header line to the output file" help="" />
-    <param name="input_header" type="boolean" checked="false" truevalue="--in-header" falsevalue="" label="Input files contain a header line (as first line)" help="" />
-    <param name="ignore_dups" type="boolean" checked="false" truevalue="--ignore-dups" falsevalue="" label="Ignore duplicated keys" help="If not set, duplicated keys in the same file will cause an error." />
-    <param name="filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields">
-        <sanitizer>
-            <valid initial="string.printable">
-                <remove value="&apos;"/>
-            </valid>
-        </sanitizer>
-    </param>
-
-  </inputs>
-  <outputs>
-    <data name="output" format="input" metadata_source="input" />
-  </outputs>
-
-<help>
+        <param name="output_header" type="boolean" checked="false" truevalue="--out-header" falsevalue="" label="Add header line to the output file" help="" />
+        <param name="input_header" type="boolean" checked="false" truevalue="--in-header" falsevalue="" label="Input files contain a header line (as first line)" help="" />
+        <param name="ignore_dups" type="boolean" checked="false" truevalue="--ignore-dups" falsevalue="" label="Ignore duplicated keys" help="If not set, duplicated keys in the same file will cause an error." />
+        <param name="filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="first_file" metadata_source="first_file" />
+    </outputs>
+    <tests>
+          <test>
+              <param name="first_file" value="multijoin1.txt" />
+              <param name="files" value="multijoin2.txt,multijoin3.txt" />
+              <param name="key_column" value="4" />
+              <param name="value_columns" value="c7,c8,c9" />
+              <param name="output_header" value="True" />
+              <output name="outfile" file="multijoin_result1.txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
 **What it does**
 
 This tool joins multiple tabular files based on a common key column.
@@ -108,12 +123,11 @@
     FBtr0300796         0         0         0        56       1296      14475          0         0         0
     ...
 
+.. class:: infomark
 
-# Input files need not be sorted.
-
------
+Input files need not be sorted.
 
-*multijoin* was written by A. Gordon (gordon at cshl dot edu)
-
-</help>
+@REFERENCES@
+]]>
+    </help>
 </tool>