--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/remove.rare.xml	Fri May 19 05:11:18 2017 -0400
@@ -0,0 +1,165 @@
+<tool profile="16.07" id="mothur_remove_rare" name="Remove.rare" version="@WRAPPER_VERSION@.0">
+    <description>Remove rare OTUs</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 "$input.otu" input_otu.dat &&
+        #if $input.source == 'list':
+            ln -s "$input.group" input.group.dat &&
+            ln -s "$input.count" input.count.dat &&
+        #end if
+
+        echo 'remove.rare(
+            #if $input.otu.is_of_type("mothur.rabund"):
+                rabund=input_otu.dat,
+            #elif $input.otu.is_of_type("mothur.sabund"):
+                sabund=input_otu.dat,
+            #elif $input.otu.is_of_type("mothur.list"):
+                list=input_otu.dat,
+                #if $input.group:
+                    group=input.group.dat,
+                #end if
+                #if $input.groups:
+                    groups=${ str($input.groups).replace(",","-") },
+                #end if
+                #if $input.count:
+                    count=input.count.dat,
+                #end if
+            #elif $input.otu.is_of_type("mothur.shared"):
+                shared=input_otu.dat,
+                bygroup=$input.bygroup,
+                #if $input.groups:
+                    groups=${ str($input.groups).replace(",","-") },
+                #end if
+            #end if
+            #if $input.label:
+                label=${ str($input.label).replace(",","-") },
+            #end if
+            nseqs=$nseqs
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="source" type="select" label="Select Input Format">
+                <option value="shared">shared</option>
+                <option value="list">list</option>
+                <option value="default">rabund or sabund</option>
+            </param>
+            <when value="shared">
+                <param name="otu" type="data" format="mothur.shared" label="shared - Otu dataset"/>
+                <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
+                    <options>
+                        <filter type="data_meta" ref="otu" key="groups"/>
+                    </options>
+                </param>
+                <param name="bygroup" type="boolean" truevalue="true" falsevalue="false" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/>
+                <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
+                    <expand macro="labeloptions"/>
+                </param>
+            </when>
+            <when value="list">
+                <param name="otu" type="data" format="mothur.list" label="list - Otu dataset"/>
+                <param name="group" type="data" optional="true" format="mothur.groups" label="group - Groups"/>
+                <param name="count" type="data" format="count_table" optional="true" label="count - Count Table" help="If you clustered with a count file, can only supply one of group or count table, not both"/>
+                <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
+                    <options>
+                        <filter type="data_meta" ref="group" key="groups"/>
+                    </options>
+                </param>
+                <param name="label" type="select" multiple="false" optional="true" label="label - OTU Labels">
+                    <expand macro="labeloptions"/>
+                </param>
+            </when>
+            <when value="default">
+                <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - Otu dataset"/>
+                <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
+                    <expand macro="labeloptions"/>
+                </param>
+            </when>
+        </conditional>
+        <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}">
+            <filter>input['source'] != 'shared'</filter>
+        </data>
+        <collection name="pick_shared" type="list" label="${tool.name} on ${on_string}: pick.shared per label">
+            <filter>input['source'] == 'shared'</filter>
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
+        </collection>
+        <data name="pick_group" format="mothur.groups" from_work_dir="input.group*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
+            <filter>input['source'] == 'list'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test with list -->
+            <param name="source" value="list"/>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with list and group file -->
+            <param name="source" value="list"/>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="groups" value="forest,pasture"/>
+            <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
+            <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with shared file -->
+            <param name="source" value="shared"/>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output_collection name="pick_shared" count="36">
+                <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with shared file and label/group select -->
+            <param name="source" value="shared"/>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="bygroup" value="true"/>
+            <param name="label" value="0.05,0.22,0.41"/>
+            <param name="groups" value="forest,pasture"/>
+            <output_collection name="pick_shared" count="3">
+                <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with rabund/sabund file -->
+            <param name="source" value="default"/>
+            <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
+            <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The remove.rare_ command reads one of the following file types: list_, rabund_, sabund_ or shared_ file. It outputs a new file after removing the rare otus.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _remove.rare: https://www.mothur.org/wiki/Remove.rare
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>