--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/count.seqs.xml	Fri May 19 05:56:44 2017 -0400
@@ -0,0 +1,104 @@
+<tool profile="16.07" id="mothur_count_seqs" name="Count.seqs" version="@WRAPPER_VERSION@.0">
+    <description>(aka make.table) counts the number of sequences represented by the representative</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 "$name" name.dat &&
+        #if $grouping.use == "yes":
+            ln -s "$grouping.group" grouping.group.dat &&
+        #end if
+
+        echo 'count.seqs(
+            name=name.dat,
+            #if $grouping.use == "yes":
+                group=grouping.group.dat,
+                #if $grouping.groups:
+                    groups=${ str($grouping.groups).replace(",","-") },
+                #end if
+            #end if
+            large=$large
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
+        <conditional name="grouping">
+            <param name="use" type="select" label="Use a Group file to include counts for groups">
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
+                <param name="groups" type="select" label="groups - Groups to display" multiple="true">
+                    <help>All groups displayed if none are selected.</help>
+                    <options>
+                        <filter type="data_meta" ref="group" key="groups"/>
+                    </options>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/>
+    </outputs>
+    <tests>
+        <test><!-- test default params -->
+            <param name="name" value="amazon.names"/>
+            <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with group file -->
+            <param name="name" value="amazon.names"/>
+            <param name="use" value="yes"/>
+            <param name="group" value="amazon.groups"/>
+            <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test> <!-- test with group file and subset of groups -->
+            <param name="name" value="amazon.names"/>
+            <param name="use" value="yes"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="groups" value="pasture"/>
+            <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test> <!-- test with group file and multiple groups -->
+            <param name="name" value="amazon.names"/>
+            <param name="use" value="yes"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="groups" value="pasture,forest"/>
+            <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown.
+
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _count.seqs: https://www.mothur.org/wiki/Count.seqs
+.. _count_table: https://www.mothur.org/wiki/Count_File
+
+v.1.21.0: Updated to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>