diff phylotype.xml @ 0:61cfe849101c 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/phylotype.xml	Fri May 19 05:59:15 2017 -0400
@@ -0,0 +1,91 @@
+<tool profile="16.07" id="mothur_phylotype" name="Phylotype" version="@WRAPPER_VERSION@.0">
+    <description>Assign sequences to OTUs based on taxonomy</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 "$taxonomy" taxonomy.dat &&
+        ln -s "$name" name.dat &&
+
+        echo 'phylotype(
+            taxonomy=taxonomy.dat
+            #if $cutoff:
+                ,cutoff=$cutoff
+            #end if
+            #if $name:
+                ,name=name.dat
+            #end if
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/>
+        <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
+            <option value="0">0</option>
+            <option value="1">1</option>
+            <option value="2">2</option>
+            <option value="3">3</option>
+            <option value="4">4</option>
+            <option value="5">5</option>
+            <option value="6">6</option>
+            <option value="7">7</option>
+            <option value="8">8</option>
+            <option value="9">9</option>
+            <option value="10">10</option>
+        </param>
+        <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if &lt; 0)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
+        <data name="sabund" format="mothur.sabund" from_work_dir="taxonomy*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
+        <data name="otulist" format="mothur.list" from_work_dir="taxonomy*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/>
+            <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/>
+            <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <param name="label" value="1,4,5"/>
+            <param name="cutoff" value="5"/>
+            <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/>
+            <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/>
+            <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
+.. _phylotype: https://www.mothur.org/wiki/Phylotype
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>