diff get.relabund.xml @ 0:4ad3ea2f8584 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.relabund.xml	Fri May 19 05:46:09 2017 -0400
@@ -0,0 +1,80 @@
+<tool profile="16.07" id="mothur_get_relabund" name="Get.relabund" version="@WRAPPER_VERSION@.0">
+    <description>Calculate the relative abundance of each otu</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.relabund(
+            shared=otu.dat,
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $groups:
+                groups=${ str($groups).replace(",","-") },
+            #end if
+            scale=$scale
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select"  multiple="true" label="groups - Groups to consider">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <param name="scale" type="select" label="scale - Scale by">
+            <option value="totalgroup" selected="true">Total Groups</option>
+            <option value="totalotu">Total OTUs</option>
+            <option value="averagegroup">Average Groups</option>
+            <option value="averageotu">Average OTUs</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="relabund" format="mothur.relabund" from_work_dir="otu*.relabund" label="${tool.name} on ${on_string}: relabund"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output name="relabund" file="amazon.an.relabund" ftype="mothur.relabund"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="label" value="0.03,0.05,0.22"/>
+            <param name="groups" value="forest"/>
+            <output name="relabund" md5="3f91820ebdf2d4c640b7d1489fd67936" ftype="mothur.relabund"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file.
+
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _get.relabund: https://www.mothur.org/wiki/Get.relabund
+
+v.1.21.0: Updated to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>