diff make.lefse.xml @ 2:5e4ee2031e00 draft

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

--- a/make.lefse.xml	Tue Sep 05 17:03:57 2017 -0400
+++ b/make.lefse.xml	Tue Mar 20 21:54:05 2018 -0400
@@ -7,33 +7,33 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$design" design.dat &&
-        ln -s "$constaxonomy" constaxonomy.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$design' design.dat &&
+ln -s '$constaxonomy' constaxonomy.dat &&
 
-        echo 'make.lefse(
-            #if $otu.is_of_type("mothur.relabund"):
-                relabund=otu.dat,
-            #else
-                shared=otu.dat,
-            #end if
-            #if $design:
-                design=design.dat,
-            #end if
-            #if $constaxonomy:
-                constaxonomy=constaxonomy.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            scale=$scale
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'make.lefse(
+    #if $otu.is_of_type("mothur.relabund"):
+        relabund=otu.dat,
+    #else
+        shared=otu.dat,
+    #end if
+    #if $design:
+        design=design.dat,
+    #end if
+    #if $constaxonomy:
+        constaxonomy=constaxonomy.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    scale=$scale
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
@@ -48,6 +48,7 @@
             <option value="averagegroup">averagegroup</option>
             <option value="averageotu">averageotu</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -57,6 +58,7 @@
         <test><!-- test with shared file and defaults -->
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with relabund file -->
@@ -64,11 +66,11 @@
             <param name="design" value="toymothur.design2" ftype="tabular"/>
             <param name="label" value="0.18"/>
             <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -78,8 +80,7 @@
 
 .. _make.lefse: https://www.mothur.org/wiki/Make.lefse
 
-]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1128/AEM.01541-09</citation>
     </citations>