diff homova.xml @ 2:2ccbfa78b831 draft

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

--- a/homova.xml	Tue Sep 05 16:49:53 2017 -0400
+++ b/homova.xml	Tue Mar 20 21:58:39 2018 -0400
@@ -7,24 +7,24 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$dist" dist.dat &&
-        ln -s "$design" design.dat &&
+## create symlinks to input datasets
+ln -s '$dist' dist.dat &&
+ln -s '$design' design.dat &&
 
-        echo 'homova(
-            phylip=dist.dat,
-            design=design.dat,
-            #if $sets:
-                sets=${ str($sets).replace(",","-") },
-            #end if
-            iters=$iters,
-            alpha=$alpha
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'homova(
+    phylip=dist.dat,
+    design=design.dat,
+    #if $sets:
+        sets=${ str($sets).replace(",","-") },
+    #end if
+    iters=$iters,
+    alpha=$alpha
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
@@ -36,6 +36,7 @@
                 <filter type="data_meta" ref="design" key="groups"/>
             </options>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -51,6 +52,7 @@
                     <has_text text="A-B"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with subsets -->
@@ -63,11 +65,11 @@
                     <has_line_matching expression="A\t.*$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -90,7 +92,7 @@
 .. _homova: https://www.mothur.org/wiki/Homova
 
 v.1.20.0: Updated to Mothur 1.33, added sets parameter
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>