diff indicator.xml @ 3:c6524e1efe12 draft

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

--- a/indicator.xml	Fri Sep 08 14:34:37 2017 -0400
+++ b/indicator.xml	Tue Mar 20 22:10:48 2018 -0400
@@ -7,40 +7,40 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        #if $withdesign.tree:
-            ln -s "$withdesign.tree" withdesign.tree.dat &&
-        #end if
-        #if $withdesign.havedesign == "yes":
-            ln -s "$withdesign.design" withdesign.design.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+#if $withdesign.tree:
+    ln -s '$withdesign.tree' withdesign.tree.dat &&
+#end if
+#if $withdesign.havedesign == "yes":
+    ln -s '$withdesign.design' withdesign.design.dat &&
+#end if
 
-        echo 'indicator(
-            #if $withdesign.tree:
-                tree=withdesign.tree.dat,
-            #end if
-            #if $otu.is_of_type("mothur.relabund"):
-                relabund=otu.dat,
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $withdesign.groups:
-                groups=${ str($withdesign.groups).replace(",","-") },
-            #end if
-            #if $withdesign.havedesign == "yes":
-                design=withdesign.design.dat,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'indicator(
+    #if $withdesign.tree:
+        tree=withdesign.tree.dat,
+    #end if
+    #if $otu.is_of_type("mothur.relabund"):
+        relabund=otu.dat,
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $withdesign.groups:
+        groups=${ str($withdesign.groups).replace(",","-") },
+    #end if
+    #if $withdesign.havedesign == "yes":
+        design=withdesign.design.dat,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| 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/relabund - OTU dataset"/>
@@ -70,6 +70,7 @@
                 </param>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -92,6 +93,7 @@
                     <has_text text="pasture"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with design input and subset of groups-->
@@ -106,6 +108,7 @@
                     <not_has_text text="pasture"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with tree input -->
@@ -120,6 +123,7 @@
                 </assert_contents>
             </output>
             <output name="tree_out" md5="a22f90898611e1f4c5d84cfe18dc6ebe"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with tree input and subset of groups -->
@@ -134,11 +138,11 @@
                 </assert_contents>
             </output>
             <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -151,7 +155,7 @@
 .. _indicator: https://www.mothur.org/wiki/Indicator
 
 v.1.22.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>