diff get.otus.xml @ 0:a1aea42f0f8e 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.otus.xml	Fri May 19 05:54:16 2017 -0400
@@ -0,0 +1,101 @@
+<tool profile="16.07" id="mothur_get_otus" name="Get.otus" version="@WRAPPER_VERSION@.0">
+    <description>Get otus containing sequences from specified 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 "$otu" otu.dat &&
+        ln -s "$group_in" group_in.dat &&
+        #if $groupnames.source == 'accnos':
+            ln -s "$groupnames.accnos_in" groupnames.accnos_in.dat &&
+        #end if
+
+        echo 'get.otus(
+            list=otu.dat,
+            group=group_in.dat
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+            #if $groupnames.source == 'groups':
+                ,groups=${ str($groupnames.groups).replace(",","-") }
+            #else
+                ,accnos=groupnames.accnos_in.dat
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param name="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
+        <conditional name="groupnames">
+            <param name="source" type="select" label="Select Group Names from">
+                <option value="groups">A List of Group Names</option>
+                <option value="accnos">A History Group Name Accnos Dataset</option>
+            </param>
+            <when value="groups">
+                <param name="groups" type="select" multiple="true" force_select="true" label="groups - Pick groups to include">
+                    <help>At least one group must be selected</help>
+                    <options>
+                        <filter type="data_meta" ref="group_in" key="groups"/>
+                    </options>
+                </param>
+            </when>
+            <when value="accnos">
+                <param name="accnos_in" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
+        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
+    </outputs>
+    <tests>
+        <test><!-- test with group file -->
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="source" value="groups"/>
+            <param name="groups" value="forest,pasture"/>
+            <output name="list_out" md5="a771e0879bbb84e2764db70f66ae1277" ftype="mothur.list"/>
+            <output name="group_out" md5="954ef97da9dcd152b912bcda19a6f96c" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with accnos file and label select -->
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="label" value="0.03"/>
+            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="source" value="accnos"/>
+            <param name="accnos_in" value="amazon.groupaccnos" ftype="mothur.accnos"/>
+            <output name="list_out" md5="2069739b1f7bbbe47cc237833450e57c" ftype="mothur.list"/>
+            <output name="group_out" md5="09ffabe975dc49f1bf251ea60c569526" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _get.otus: https://www.mothur.org/wiki/Get.otus
+
+v.1.20.0: Updated to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>