diff pcoa.xml @ 0:57b46e1032ad draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pcoa.xml	Fri May 19 05:01:28 2017 -0400
@@ -0,0 +1,54 @@
+<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="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$phylip" phylip.dat &&
+
+        echo 'pcoa(
+            phylip=phylip.dat,
+            metric=$metric
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="phylip" type="data" format="mothur.dist,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>
+        <expand macro="logfile-output"/>
+        <data name="pcoa" format="mothur.axes" from_work_dir="phylip*.pcoa.axes" label="${tool.name} on ${on_string}: pcoa.axes"/>
+        <data name="loadings" format="tabular" from_work_dir="phylip*.pcoa.loadings" label="${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 Documentation**
+
+The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.
+
+.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _pcoa: https://www.mothur.org/wiki/Pcoa
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>