diff get.otulist.xml @ 0:2e6fb8f23d5e 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.otulist.xml	Fri May 19 05:52:08 2017 -0400
@@ -0,0 +1,75 @@
+<tool profile="16.07" id="mothur_get_otulist" name="Get.otulist" version="@WRAPPER_VERSION@.0">
+    <description>Get otus for each distance in a otu list</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.otulist(
+            list=otu.dat,
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            sort=$sort
+        )'
+        | 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" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected.">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="sort" type="select" label="sort - select the output format" help="If otu is selected the output will be otu number followed by the list of names in that otu. If name is selected the output will be a sequence name followed by its otu number">
+            <option value="otu" selected="true">otu</option>
+            <option value="name">name</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="otufiles" type="list" label="${tool.name} on ${on_string}: OTUs per label">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu" format="mothur.list"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <output_collection name="otufiles" count="36">
+                <element name="0.22" md5="9dfa8c449a45d66e7ae6b30b34a821cb" ftype="mothur.list"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="label" value="0.03,0.38,0.41,0.45"/>
+            <output_collection name="otufiles" count="4">
+                <element name="0.41" md5="b40486b3739a6d5b86459dc17a23c253" ftype="mothur.list"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU.
+
+.. _get.otulist: https://www.mothur.org/wiki/Get.otulist
+
+v.1.20.0: Updated to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>