diff get.coremicrobiome.xml @ 2:a1d38f9902d9 draft

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

--- a/get.coremicrobiome.xml	Tue Sep 05 16:57:07 2017 -0400
+++ b/get.coremicrobiome.xml	Tue Mar 20 22:04:46 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 "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
 
-        echo 'get.coremicrobiome(
-            #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 $groups:
-                ,groups=${ str($groups).replace(",","-") }
-            #end if
-            #if $abundance:
-                ,abundance=$abundance
-            #end if
-            #if $samples:
-                ,samples=$samples
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.coremicrobiome(
+    #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 $groups:
+        ,groups=${ str($groups).replace(",","-") }
+    #end if
+    #if $abundance:
+        ,abundance=$abundance
+    #end if
+    #if $samples:
+        ,samples=$samples
+    #end if
+)'
+| 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 - OTU Shared or Relabund"/>
@@ -51,6 +51,7 @@
             <option value="fraction" selected="true">fraction</option>
             <option value="count">count</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -68,6 +69,7 @@
             <output_collection name="core_microbiome" count="36">
                 <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list output and label and group select-->
@@ -81,11 +83,11 @@
             <output_collection name="core_microbiome_list" count="3">
                 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -97,7 +99,6 @@
 
 v1.27.0: Updated to Mothur 1.33
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>