diff make.lookup.xml @ 3:91652222f7b4 draft

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

--- a/make.lookup.xml	Fri Sep 08 14:55:56 2017 -0400
+++ b/make.lookup.xml	Tue Mar 20 22:15:22 2018 -0400
@@ -7,26 +7,26 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        #import re
-        ## create symlinks to input datasets
-        ln -s "$reference.template" reference.template.dat &&
-        ln -s "$flow" flow.dat &&
-        ln -s "$error" error.dat &&
+#import re
+## create symlinks to input datasets
+ln -s '$reference.template' reference.template.dat &&
+ln -s '$flow' flow.dat &&
+ln -s '$error' error.dat &&
 
-        echo 'make.lookup(
-            reference=reference.template.dat,
-            flow=flow.dat,
-            error=error.dat,
-            order=$order,
-            barcode=$re.sub("[^ACTG]","",str($barcode)),
-            key=$re.sub("[^ACTG]","",str($key)),
-            threshold=$threshold
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'make.lookup(
+    reference=reference.template.dat,
+    flow=flow.dat,
+    error=error.dat,
+    order=$order,
+    barcode=$re.sub("[^ACTG]","",str($barcode)),
+    key=$re.sub("[^ACTG]","",str($key)),
+    threshold=$threshold
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="reference">
@@ -53,6 +53,7 @@
         <param name="barcode" type="text" value="AACCGTGTC" label="barcode - provide the barcode sequence"/>
         <param name="key" type="text" value="TCAG" label="key - provide the key sequence"/>
         <param name="threshold" type="integer" value="10000" min="0" label="threshold - " help=""/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -69,6 +70,7 @@
                     <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test sanitizers -->
@@ -83,11 +85,11 @@
                     <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -97,8 +99,7 @@
 
 .. _make.lookup: https://www.mothur.org/wiki/Make.lookup
 
-]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1128/AEM.01541-09</citation>
     </citations>