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

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/deunique.tree.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,55 @@
+<tool profile="16.07" id="mothur_deunique_tree" name="Deunique.tree" version="@WRAPPER_VERSION@.0">
+    <description>Reinsert the redundant sequence identiers back into a unique tree.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'deunique.tree(
+            tree=$tree,
+            name=$names
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$tree" &&
+        mv mothur.*.logfile "$logfile" &&
+        mv \${prefix%.dat}*.deunique.tre "$out_tree"
+    ]]></command>
+    <inputs>
+        <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/>
+        <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="out_tree" format_source="tree" label="${tool.name} on ${on_string}: deunique.tre"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="tree" value="treetest.tre"/>
+            <param name="names" value="treetest.names"/>
+            <output name="out_tree" file="treetest.deunique.tre"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+
+**Command Documenation**
+
+The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file.
+
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _deunique.tree: http://www.mothur.org/wiki/Deunique.tree
+
+v1.21.0: Updated to Mothur 1.33
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>