diff tools/mothur/normalize.shared.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/normalize.shared.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,90 @@
+<tool profile="16.07" id="mothur_normalize_shared" name="Normalize.shared" version="@WRAPPER_VERSION@.0">
+    <description>Normalize the number of sequences per group to a specified level</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'normalize.shared(
+            #if $otu.is_of_type("mothur.relabund"):
+                relabund=$otu
+            #elif $otu.is_of_type("mothur.shared"):
+                shared=$otu,
+                makerelabund=$makerelabund
+            #end if
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+            #if $groups:
+                ,groups=${ str($groups).replace(",","-") }
+            #end if
+            #if $method:
+                ,method=${ str($method).replace(",","-") }
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$otu" &&
+        mv mothur.*.logfile "$logfile" &&
+        mv \${prefix%.dat}*.shared .
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select" label="groups - Groups to include" multiple="true">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <param name="method" type="select" label="method - Normalization method">
+            <option value="totalgroup" selected="true">Total Group</option>
+            <option value="zscore">Z Score</option>
+        </param>
+        <param name="makerelabund" type="boolean" truevalue="true" falsevalue="false" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: norm.shared files collection">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test default settings -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output_collection name="sharedfiles" count="36">
+                <element name="0.26.norm" md5="73ad51ce74e5b3efbc1d9ec8ed6e1c07" ftype="mothur.shared"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test default settings -->
+            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
+            <param name="label" value="0.03,0.05,0.22,0.26"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="method" value="zscore"/>
+            <output_collection name="sharedfiles" count="4">
+                <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The normalize.shared_ command normalizes the number of sequences per group to a specified level.  The input is a shared_ or relabund_ file.
+
+.. _shared: http://www.mothur.org/wiki/Shared_file
+.. _relabund: http://www.mothur.org/wiki/Get.relabund
+.. _normalize.shared: http://www.mothur.org/wiki/Normalize.shared
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>