--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_corr.xml	Fri Apr 27 09:48:24 2018 -0400
@@ -0,0 +1,79 @@
+<tool id="plot_correlation" name="Plot correlations" version="0.1.3">
+    <description>for multiple samples</description>
+    <requirements>
+        <requirement type="package" version="0.8.1">seaborn</requirement>
+        <requirement type="package" version="6.7">click</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/plot_corr.py'
+#echo "".join(["'%s' " % f for f in $input_files])
+-c $c
+--labels '$labels'
+#if $plot_type != "None"
+    --plot_path output.$plot_type
+#end if
+--correlation_matrix_path $tab_output
+--method $method
+--skiprows $skiprows
+#if $input_files[0].ext == 'csv'
+--sep ","
+#end if
+#if $plot_type != "None"
+    && mv output.$plot_type plot
+#end if
+    ]]></command>
+<configfiles>
+    <configfile name="labels">#for f in $input_files
+$f.element_identifier
+#end for</configfile>
+</configfiles>
+    <inputs>
+        <param name="input_files" type="data" multiple="true" format="tabular,csv" label="Select the files for which to calculate the correlation"/>
+        <param argument="-c" type="data_column" data_ref="input_files" value="1" label="Select the numeric column to use"/>
+        <param argument="--skiprows" type="integer" min="0" value="0" label="Skip the first N rows" help="Make sure that all values are numeric"/>
+        <param argument="--plot_type" type="select" label="Select the type of plot to produce">
+            <option value="pdf">PDF</option>
+            <option value="png">PNG</option>
+            <option value="None">Don't output plot</option>
+        </param>
+        <param argument="--method" type="select" label="Select the correlation method">
+            <option value="pearson">Pearson Correlation</option>
+            <option value="spearman">Spearman Correlation</option>
+            <option value="kendall">Kendall-Tau Correlation</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="plot_output" format="pdf" from_work_dir="plot" label="${tool.name} plot on ${on_string}">
+            <filter>str(plot_type) != "None"</filter>
+            <change_format>
+                <when input="plot_type" value="png" format="png"/>
+            </change_format>
+        </data>
+        <data name="tab_output" format="tabular" label="${tool.name} table on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_files" value="1.txt,2.txt,3.txt" ftype="tabular"/>
+            <output name="plot_output" value="corr.pdf" ftype="pdf"/>
+            <output name="tab_output" value="corr.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input_files" value="1.txt,2.txt,3.txt" ftype="tabular"/>
+            <param name="plot_type" value="png"/>
+            <output name="plot_output" value="corr.png" ftype="png"/>
+            <output name="tab_output" value="corr.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+------------
+
+This tool calculates the correlation for a selected colum across many datasets.
+
+Example output:
+---------------
+
+.. image:: $PATH_TO_IMAGES/corr.png
+
+        ]]></help>
+</tool>