diff count.groups.xml @ 0:6f454356bfc7 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/count.groups.xml	Fri May 19 05:44:34 2017 -0400
@@ -0,0 +1,97 @@
+<tool profile="16.07" id="mothur_count_groups" name="Count.groups" version="@WRAPPER_VERSION@.0">
+    <description>counts the number of sequences represented by a specific group or set of groups</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 "$group" group.dat &&
+        #if $groupnames.source == "accnos":
+            ln -s "$groupnames.accnos" groupnames.accnos.dat &&
+        #end if
+
+        echo 'count.groups(
+            #if $group.is_of_type("mothur.shared"):
+                shared=group.dat
+            #elif $group.is_of_type("mothur.count_table"):
+                count=group.dat
+            #else:
+                group=group.dat
+            #end if
+            #if $groupnames.source == "groups":
+                #if $groupnames.groups:
+                    ,groups=$groupnames.groups
+                #end if
+            #elif $groupnames.source == "accnos":
+                #if $groupnames.accnos:
+                    ,accnos=groupnames.accnos.dat
+                #end if
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log &&
+
+        ## parse relevant tool output from logfile to file
+        cat mothur.*.logfile
+        | head -n-7
+        | sed '1,29d'
+        > "$grp_count"
+    ]]></command>
+    <inputs>
+        <param name="group" type="data" format="mothur.groups,mothur.shared,mothur.count_table" label="group, shared, or count_table - Group file for sequence count"/>
+        <conditional name="groupnames">
+            <param name="source" type="select" label="Filter group names">
+                <option value="none">Report on All Groups</option>
+                <option value="groups">A List of Group Names</option>
+                <option value="accnos">A History Group Name Accnos Dataset</option>
+            </param>
+            <when value="none"/>
+            <when value="groups">
+                <param name="groups" type="select" label="groups - Pick groups to include" 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="accnos">
+                <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="grp_count" format="tabular" label="${tool.name} on ${on_string}: group.count"/>
+        <data name="summary" format="tabular" from_work_dir="group*.summary" label="${tool.name} on ${on_string}: summary"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="groups" value="forest,pasture"/>
+            <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
+            <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.
+
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _count.groups: https://www.mothur.org/wiki/Count.groups
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>