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

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/pcoa.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,53 @@
+<tool profile="16.07" id="mothur_pcoa" name="Pcoa" version="@WRAPPER_VERSION@.0">
+    <description>Principal Coordinate Analysis for a distance matrix</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'pcoa(
+            phylip=$phylip,
+            metric=$metric
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$phylip" &&
+        mv mothur.*.logfile "$logfile" &&
+        mv \${prefix%.dat}*.pcoa.axes "$pcoa" &&
+        mv \${prefix%.dat}*.pcoa.loadings "$loadings"
+    ]]></command>
+    <inputs>
+        <param name="phylip" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
+        <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="pcoa" format="mothur.axes" label="${tool.name} on ${on_string}: pcoa.axes"/>
+        <data name="loadings" format="tabular" label="${tool.name} on ${on_string}: loadings"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="phylip" value="amazon.dist"/>
+            <output name="pcoa" file="amazon.pcoa.axes"/>
+            <output name="loadings" file="amazon.pcoa.loadings"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.
+
+.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _pcoa: http://www.mothur.org/wiki/Pcoa
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>