diff get.group.xml @ 0:200b088eaf93 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/get.group.xml	Fri May 19 05:57:15 2017 -0400
@@ -0,0 +1,57 @@
+<tool profile="16.07" id="mothur_get_group" name="Get.group" version="@WRAPPER_VERSION@.0">
+    <description>group names from shared or from list and group</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 "$otu" otu.dat &&
+
+        echo 'get.group(
+            shared=otu.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log &&
+
+        ## parse relevant output from logfile to file
+        cat mothur.*.logfile
+        | head -n-6
+        | sed '1,29d'
+        > "$bootgroups"
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="bootgroups" format="mothur.groups" label="${tool.name} on ${on_string}: bootGroups"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The get.group_ command generate principle components plot data.
+
+.. _get.group: https://www.mothur.org/wiki/Get.group
+
+v.1.20.0: Updated to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>