diff unifrac.unweighted.xml @ 2:c26d24a77e85 draft

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

--- a/unifrac.unweighted.xml	Tue Sep 05 16:51:05 2017 -0400
+++ b/unifrac.unweighted.xml	Tue Mar 20 22:05:47 2018 -0400
@@ -7,48 +7,48 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$tree" tree.dat &&
-        ln -s "$group" group.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$tree' tree.dat &&
+ln -s '$group' group.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'unifrac.unweighted(
-            tree=tree.dat,
-            #if $group:
-                group=group.dat,
-                #if $groups:
-                    groups=${ str($groups).replace(",","-") },
-                #end if
-            #end if
-            #if $name:
-                name=name.dat,
-            #end if
-            iters=$iters,
-            #if $subsampling.use == "yes":
-                #if $subsampling.subsample:
-                    subsample=$subsampling.subsample,
-                #else
-                    subsample=T,
-                #end if
-                consensus=$subsampling.consensus,
-            #else
-                random=$random,
-            #end if
-            #if $distance:
-                distance=$distance,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            root=$root,
-            processors='\${GALAXY_SLOTS:-1}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'unifrac.unweighted(
+    tree=tree.dat,
+    #if $group:
+        group=group.dat,
+        #if $groups:
+            groups=${ str($groups).replace(",","-") },
+        #end if
+    #end if
+    #if $name:
+        name=name.dat,
+    #end if
+    iters=$iters,
+    #if $subsampling.use == "yes":
+        #if $subsampling.subsample:
+            subsample=$subsampling.subsample,
+        #else
+            subsample=T,
+        #end if
+        consensus=$subsampling.consensus,
+    #else
+        random=$random,
+    #end if
+    #if $distance:
+        distance=$distance,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    root=$root,
+    processors='\${GALAXY_SLOTS:-1}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="tree" type="data" format="mothur.tre" label="tree - Tree"/>
@@ -79,6 +79,7 @@
         </param>
         <param name="root" type="boolean" truevalue="true" falsevalue="false" checked="false" label="root - the entire root in your calculations"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -118,6 +119,7 @@
             <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
             <output name="summary" md5="33917fcb36e815ed8924f2ea2729bdc1" ftype="tabular"/>
             <output name="dist" md5="ce65f7d1d2aeb492d8a5373ca18ed5b0" ftype="mothur.lower.dist"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with random and no subsampling -->
@@ -125,6 +127,7 @@
             <param name="random" value="true"/>
             <output name="summary" md5="6aff35274802c4727cbbbc084b7d2dca" ftype="tabular"/>
             <output name="unweighted" md5="9f52d2bd4c5de4c459ae314b6ed83b7a" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group file and group select -->
@@ -134,6 +137,7 @@
             <param name="distance" value="square"/>
             <output name="summary" md5="a4a0a2faf75cb15bdb049c368dcbe73a" ftype="tabular"/>
             <output name="dist" md5="d215db402049db87cac629470301d5c6" ftype="mothur.square.dist"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with subsample and consensus -->
@@ -174,11 +178,11 @@
                     <has_text text="C"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -188,7 +192,6 @@
 
 .. _unifrac.unweighted: https://www.mothur.org/wiki/Unifrac.unweighted
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>