diff merge.sfffiles.xml @ 2:e0d980518148 draft

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

--- a/merge.sfffiles.xml	Tue Sep 05 17:14:57 2017 -0400
+++ b/merge.sfffiles.xml	Tue Mar 20 22:10:34 2018 -0400
@@ -7,24 +7,25 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        #for $i in $input:
-            ln -s "$i" input${input.index($i)}.dat &&
-        #end for
+## create symlinks to input datasets
+#for $i in $input:
+    ln -s '$i' input${input.index($i)}.dat &&
+#end for
 
-        echo 'merge.sfffiles(
-            sff=#for $i in $input#input${input.index($i)}.dat-#end for#,
-            output=$output
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | sed 's/-,/,/g'
-        | mothur
-        | tee mothur.out.log
+echo 'merge.sfffiles(
+    sff=#for $i in $input#input${input.index($i)}.dat-#end for#,
+    output=$output
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| sed 's/-,/,/g'
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -38,11 +39,11 @@
                     <has_text text="FLP3FBN01ELBSX"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -54,7 +55,6 @@
 
 .. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>