diff summary.single.xml @ 4:c4db2a4fdb42 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4

--- a/summary.single.xml	Tue Sep 05 16:09:32 2017 -0400
+++ b/summary.single.xml	Wed Feb 14 10:10:10 2018 -0500
@@ -7,51 +7,51 @@
     <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 'summary.single(
-            #if $otu.is_of_type("mothur.rabund"):
-                rabund=otu.dat
-            #elif $otu.is_of_type("mothur.sabund"):
-                sabund=otu.dat
-            #elif $otu.is_of_type("mothur.list"):
-                list=otu.dat
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat,
-                groupmode=$groupmode
-            #end if
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-            #if $calc:
-                ,calc=${ str($calc).replace(",","-") }
-            #end if
-            #if $abund:
-                ,abund=$abund
-            #end if
-            #if $size:
-                ,size=$size
-            #end if
-            #if $subsample.use == 'yes':
-                #if $subsample.subsample:
-                    ,subsample=$subsample.subsample
-                #else
-                    ,subsample=T
-                #end if
-                #if $subsample.iters:
-                    ,iters=$subsample.iters
-                #end if
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
-            && mv otu.*ave-std.summary otu.ave-std
+echo 'summary.single(
+    #if $otu.is_of_type("mothur.rabund"):
+        rabund=otu.dat
+    #elif $otu.is_of_type("mothur.sabund"):
+        sabund=otu.dat
+    #elif $otu.is_of_type("mothur.list"):
+        list=otu.dat
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat,
+        groupmode=$groupmode
+    #end if
+    #if $label:
+        ,label=${ str($label).replace(",","-") }
+    #end if
+    #if $calc:
+        ,calc=${ str($calc).replace(",","-") }
+    #end if
+    #if $abund:
+        ,abund=$abund
+    #end if
+    #if $size:
+        ,size=$size
+    #end if
+    #if $subsample.use == 'yes':
+        #if $subsample.subsample:
+            ,subsample=$subsample.subsample
+        #else
+            ,subsample=T
         #end if
+        #if $subsample.iters:
+            ,iters=$subsample.iters
+        #end if
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+#if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
+    && mv otu.*ave_std.summary otu.ave-std
+#end if
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
@@ -156,8 +156,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -167,7 +166,7 @@
 
 .. _group: https://www.mothur.org/wiki/Group_file
 .. _summary.single: https://www.mothur.org/wiki/Summary.single
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>