diff heatmap.bin.xml @ 2:ac2fa6a167ad draft

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

--- a/heatmap.bin.xml	Tue Sep 05 17:11:33 2017 -0400
+++ b/heatmap.bin.xml	Tue Mar 20 22:22:20 2018 -0400
@@ -7,37 +7,37 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.otu" input_otu.dat &&
+## create symlinks to input datasets
+ln -s '$input.otu' input_otu.dat &&
 
-        echo 'heatmap.bin(
-            #if $input.otu.is_of_type("mothur.rabund"):
-                rabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.sabund"):
-                sabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.list"):
-                list=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.relabund"):
-                relabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.shared"):
-                shared=input_otu.dat,
-            #end if
-            #if $input.has_groups == 'yes' and $input.groups:
-                groups=${ str($input.groups).replace(",","-") },
-            #end if
-            #if $input.label:
-                label=${ str($input.label).replace(",","-") },
-            #end if
-            scale=$scale,
-            sorted=$sorted,
-            numotu=$numotu,
-            fontsize=$fontsize
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'heatmap.bin(
+    #if $input.otu.is_of_type("mothur.rabund"):
+        rabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.sabund"):
+        sabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.list"):
+        list=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.relabund"):
+        relabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.shared"):
+        shared=input_otu.dat,
+    #end if
+    #if $input.has_groups == 'yes' and $input.groups:
+        groups=${ str($input.groups).replace(",","-") },
+    #end if
+    #if $input.label:
+        label=${ str($input.label).replace(",","-") },
+    #end if
+    scale=$scale,
+    sorted=$sorted,
+    numotu=$numotu,
+    fontsize=$fontsize
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -76,6 +76,7 @@
         </param>
         <param name="numotu" type="integer" value="0" min="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
         <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -90,6 +91,7 @@
             <output_collection name="heatmaps" count="36">
                 <element name="0.26.heatmap" md5="8f0d5cb95808115e50729e6df60629cc"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -100,6 +102,7 @@
             <output_collection name="heatmaps" count="1">
                 <element name="0.26.heatmap" md5="b2b46b7e55f55e2b260cd6dc6ccb4485"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -113,11 +116,11 @@
             <output_collection name="heatmaps" count="3">
                 <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -131,7 +134,7 @@
 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
 
 v.1.21.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>