diff tools/mothur/mantel.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/mantel.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,64 @@
+<tool profile="16.07" id="mothur_mantel" name="Mantel" version="@WRAPPER_VERSION@.0">
+    <description>Mantel correlation coefficient between two matrices.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+       echo 'mantel(
+            phylip1=$dist,
+            phylip2=$dist2,
+            method=$method,
+            iters=$iters
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$dist" &&
+        mv mothur.*.logfile "$logfile" &&
+        mv \${prefix%.dat}*.mantel "$mantel"
+    ]]></command>
+    <inputs>
+        <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+        <param name="dist2" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip2 - Distance Matrix"/>
+        <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
+                <option value="pearson" selected="true">pearson</option>
+                <option value="spearman">spearman</option>
+                <option value="kendall">kendall</option>
+        </param>
+        <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="mantel" format="tabular" label="${tool.name} on ${on_string}: mantel"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dist" value="veg.dist"/>
+            <param name="dist2" value="env.dist"/>
+            <output name="mantel" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="^Mantel\tpValue$"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The mantel_ command calculates the Mantel correlation coefficient between two matrices_.
+
+.. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _mantel: http://www.mothur.org/wiki/Mantel
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>