diff list.otulabels.xml @ 2:88e8819fb923 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- a/list.otulabels.xml	Tue Sep 05 17:03:06 2017 -0400
+++ b/list.otulabels.xml	Tue Mar 20 22:16:21 2018 -0400
@@ -7,29 +7,29 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
 
-        echo 'list.otulabels(
-            #if $otu.is_of_type("mothur.relabund"):
-                relabund=otu.dat
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat
-            #else
-                list=otu.dat
-            #end if
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-            #if $groups:
-                ,groups=${ str($groups).replace(",","-") }
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'list.otulabels(
+    #if $otu.is_of_type("mothur.relabund"):
+        relabund=otu.dat
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat
+    #else
+        list=otu.dat
+    #end if
+    #if $label:
+        ,label=${ str($label).replace(",","-") }
+    #end if
+    #if $groups:
+        ,groups=${ str($groups).replace(",","-") }
+    #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,mothur.list" label="list or shared or relabund - OTU List or Shared or Relabund"/>
@@ -41,6 +41,7 @@
                 <filter type="data_meta" ref="otu" key="groups"/>
             </options>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -56,6 +57,7 @@
                 <element name="unique" md5="c901cebfbc87559f1667546111408a22" ftype="mothur.otulabels"/>
                 <element name="0.55" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.otulabels"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group select -->
@@ -65,28 +67,29 @@
             <output_collection name="otulabels" count="36">
                 <element name="unique" md5="8a4d85496fdcfdf99337129989350e7e" ftype="mothur.otulabels"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
 
-The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands.
+The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otus_ or remove.otulabels_ commands
 
 .. _list.otulabels: https://www.mothur.org/wiki/List.otulabels
 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
 .. _otu.association: https://www.mothur.org/wiki/Otu.association
 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
+.. _get.otus: https://www.mothur.org/wiki/Get.otus
 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _relabund: https://www.mothur.org/wiki/Get.relabund
 
 v.1.27.0: Updated to mothur 1.33, added list file for otu
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>