diff get.rabund.xml @ 0:fc3330ca7c70 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.rabund.xml	Fri May 19 05:09:39 2017 -0400
@@ -0,0 +1,76 @@
+<tool profile="16.07" id="mothur_get_rabund" name="Get.rabund" version="@WRAPPER_VERSION@.0">
+    <description>Get rabund from a otu list or sabund</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 "$count" count.dat &&
+        ln -s "$otu" otu.dat &&
+
+        echo 'get.rabund(
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            #if $otu.is_of_type("mothur.list"):
+                list=otu.dat,
+            #elif $otu.is_of_type("mothur.sabund"):
+                sabund=otu.dat,
+            #end if
+            sorted=$sorted
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/>
+        <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance" help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="rabund" format="mothur.rabund" from_work_dir="otu*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
+    </outputs>
+    <tests>
+        <test><!-- test sabund input -->
+            <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
+            <param name="label" value="0.03,0.05"/>
+            <output name="rabund" file="amazon.an.rabund2" ftype="mothur.rabund"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test otu list input -->
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The get.rabund_ command generates an rabund_ file from a list_ or sabund_ file.
+
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _list: https://www.mothur.org/wiki/List_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
+.. _get.rabund: https://www.mothur.org/wiki/Get.rabund
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>