diff deunique.tree.xml @ 0:90796e3ff3ef 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/deunique.tree.xml	Fri May 19 05:28:47 2017 -0400
@@ -0,0 +1,58 @@
+<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="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$tree" tree.dat &&
+        ln -s "$names" names.dat &&
+
+        echo 'deunique.tree(
+            tree=tree.dat,
+            name=names.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></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>
+        <expand macro="logfile-output"/>
+        <data name="out_tree" format_source="tree" from_work_dir="tree*.deunique.tre" 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 Documentation**
+
+The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file.
+
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree
+
+v1.21.0: Updated to Mothur 1.33
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>