--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/join_files_by_id.xml	Wed Aug 09 17:44:54 2017 -0400
@@ -0,0 +1,124 @@
+<tool id="join_files_by_id" name="Join datasets by identifier column" version="1.0">
+    <requirements>
+        <requirement type="package" version="1.10.4">r-data.table</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/join_files.R'
+--out='$out_file1'
+--he='$header'
+--jc='$field'
+--sep='$delimiter'
+--nc='$null_str'
+--in='$input1'
+#for $q in $queries
+    --in='${q.input}'
+#end for
+    ]]></command>
+    <inputs>
+        <param name="header" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Header" help="If header is true, the column name used for joining need to be the same in all datasets"/>
+        <param name="delimiter" type="select" label="Delimited by">
+            <option value="ta">Tab</option>
+            <option value="do">Dot</option>
+            <option value="co">Comma</option>
+            <option value="un">Underscore</option>
+            <option value="da">Dash</option>
+            <option value="sp">Space</option>
+        </param>
+        <param name="null_str" type="select" label="Select mismatch character">
+            <option value="0">0</option>
+            <option value="-">-</option>
+            <option value="">"empty"</option>
+            <option value="NA">NA</option>
+        </param>
+        <param name="input1" type="data" format="tabular" label="Select table" help="Single dataset selection only to preserve the order"/>
+        <repeat name="queries" min="1" title="Select table">
+            <param name="input" type="data" format="tabular" label="Select table" help="Single dataset selection only to preserve the order"/>
+        </repeat>
+        <param name="field" type="data_column" data_ref="input1" label="Column used for joining" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="header" value="1"/>
+            <param name="null_str" value="0"/>
+            <param name="delimiter" value="ta"/>
+            <param name="input1" value="df1.txt"/>
+            <repeat name="queries">
+                <param name="input" value="df2.txt"/>
+            </repeat>
+            <repeat name="queries">
+                <param name="input" value="df3.txt"/>
+            </repeat>
+            <param name="field" value="1"/>
+            <output name="out_file1" file="df.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Joins datasets by identifier column
+
+-----
+
+'''Example'''
+
+Dataset 1:
+
++--------+--------+---------+
+| name   | counts | percent |
++========+========+=========+
+| gene 1 |   10   |   0.3   |
++--------+--------+---------+
+| gene 2 |   20   |   0.2   |
++--------+--------+---------+
+| gene 3 |   20   |   0.2   |
++--------+--------+---------+
+
+
+and Dataset 2:
+
++--------+--------+---------+
+| name   | counts | percent |
++========+========+=========+
+| gene 1 |   13   |   0.5   |
++--------+--------+---------+
+| gene 4 |    4   |   0.4   |
++--------+--------+---------+
+
+
+and Dataset 3:
+
++--------+--------+---------+
+| name   | counts | percent |
++========+========+=========+
+| gene 1 |   10   |   0.3   |
++--------+--------+---------+
+| gene 3 |   12   |   0.2   |
++--------+--------+---------+
+| gene 4 |    4   |   0.4   |
++--------+--------+---------+
+| gene 5 |   19   |   0.6   |
++--------+--------+---------+
+
+
+will result in the following:
+
++--------+--------+---------+--------+---------+--------+---------+
+| name   | counts | percent | counts | percent | counts | percent |
++========+========+=========+========+=========+========+=========+
+| gene 1 |   10   |   0.3   |   13   |   0.5   |   10   |   0.3   |
++--------+--------+---------+--------+---------+--------+---------+
+| gene 2 |   20   |   0.2   |    0   |    0    |    0   |    0    |
++--------+--------+---------+--------+---------+--------+---------+
+| gene 3 |   12   |   0.2   |    0   |    0    |   12   |   0.2   |
++--------+--------+---------+--------+---------+--------+---------+
+| gene 4 |    0   |    0    |    4   |   0.4   |    4   |   0.4   |
++--------+--------+---------+--------+---------+--------+---------+
+| gene 5 |    0   |    0    |    0   |    0    |   19   |   0.6   |
++--------+--------+---------+--------+---------+--------+---------+
+
+For help contact: jochen.bick@usys.ethz.ch
+    ]]></help>
+</tool>