diff libshuff.xml @ 2:ffe8649e5434 draft

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

--- a/libshuff.xml	Tue Sep 05 17:05:02 2017 -0400
+++ b/libshuff.xml	Tue Mar 20 21:59:44 2018 -0400
@@ -7,30 +7,30 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$dist" dist.dat &&
-        ln -s "$group" group.dat &&
+## create symlinks to input datasets
+ln -s '$dist' dist.dat &&
+ln -s '$group' group.dat &&
 
-        echo 'libshuff(
-            phylip=dist.dat,
-            group=group.dat,
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            sim=$sim,
-            #if $form.form2 == "discrete":
-                step=$form.step,
-                #if $form.cutoff:
-                    cutoff=$form.cutoff,
-                #end if
-            #end if
-            iters=$iters
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'libshuff(
+    phylip=dist.dat,
+    group=group.dat,
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    sim=$sim,
+    #if $form.form2 == "discrete":
+        step=$form.step,
+        #if $form.cutoff:
+            cutoff=$form.cutoff,
+        #end if
+    #end if
+    iters=$iters
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
@@ -53,6 +53,7 @@
                 <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -76,6 +77,7 @@
                     <has_text text="pasture-forest"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -98,11 +100,11 @@
                     <has_text text="pasture-forest"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -113,7 +115,6 @@
 
 .. _libshuff: https://www.mothur.org/wiki/Libshuff
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>