diff otu.association.xml @ 0:4b4ca5a8e3e2 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/otu.association.xml	Fri May 19 05:51:08 2017 -0400
@@ -0,0 +1,102 @@
+<tool profile="16.07" id="mothur_otu_association" name="Otu.association" version="@WRAPPER_VERSION@.0">
+    <description>Calculate the correlation coefficient for the otus</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 "$otu" otu.dat &&
+        ln -s "$metadata" metadata.dat &&
+
+        echo 'otu.association(
+            #if $otu.is_of_type("mothur.relabund"):
+                relabund=otu.dat
+            #elif $otu.is_of_type("mothur.shared"):
+                shared=otu.dat
+            #end if
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+            #if $groups:
+                ,groups=${ str($groups).replace(",","-") }
+            #end if
+            #if $method:
+                ,method=$method
+            #end if
+            #if $metadata:
+                ,metadata=metadata.dat
+            #end if
+            #if $cutoff:
+                ,cutoff=$cutoff
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></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" help="By default all labels are used">
+            <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="pearson" selected="true">pearson</option>
+            <option value="spearman">spearman</option>
+            <option value="kendall">kendall</option>
+        </param>
+        <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/>
+        <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="correlations" type="list" label="${tool.name} on ${on_string}: correlation coefficient files per OTU label">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu\.corr" format="mothur.otu.corr"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test with shared file and default settings -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output_collection name="correlations" count="36">
+                <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with relabund file and label and group select -->
+            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
+            <param name="method" value="kendall"/>
+            <param name="label" value="0.03,0.05,0.36,0.41,0.55"/>
+            <param name="groups" value="forest,pasture"/>
+            <output_collection name="correlations" count="5">
+                <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The otu.association_ command calculates the correlation coefficient for the otus in a shared_ or relabund_ file.
+
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _relabund: https://www.mothur.org/wiki/Get.relabund
+.. _otu.association: https://www.mothur.org/wiki/Otu.association
+
+v.1.25.0: Updated to mothur 1.33, added cutoff option
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>