diff pca.xml @ 0:56400efc6755 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/pca.xml	Fri May 19 05:32:07 2017 -0400
@@ -0,0 +1,83 @@
+<tool profile="16.07" id="mothur_pca" name="Pca" version="@WRAPPER_VERSION@.0">
+    <description>Principal Coordinate Analysis for a shared file</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 "$otu" otu.dat &&
+
+        echo 'pca(
+            #if $otu.is_of_type("mothur.relabund"):
+                relabund=otu.dat,
+            #elif $otu.is_of_type("mothur.shared"):
+                shared=otu.dat,
+            #end if
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $groups:
+                groups=${ str($groups).replace(",","-") },
+            #end if
+            metric=$metric
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="pca_axes" type="list" label="${tool.name} on ${on_string}: pca.axes">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.axes" format="mothur.axes"/>
+        </collection>
+        <collection name="pca_loadings" type="list" label="${tool.name} on ${on_string}: pca.loadings">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.loadings" format="txt"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="label" value="0.22,0.55"/>
+            <output_collection name="pca_axes" count="2">
+                <element name="0.22" md5="4e32155fcfefe7d2f45b896d26b36409" ftype="mothur.axes"/>
+            </output_collection>
+            <output_collection name="pca_loadings" count="2">
+                <element name="0.55" md5="8c76b60484ffcab2ef7230e29071dd51" ftype="txt"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The pca_ command generate principle components plot data for a shared_ or relabund_ file.
+
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _relabund: https://www.mothur.org/wiki/Get.relabund
+.. _pca: https://www.mothur.org/wiki/Pca
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>