diff merge.files.xml @ 2:669032cdc951 draft

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

--- a/merge.files.xml	Tue Sep 05 16:58:03 2017 -0400
+++ b/merge.files.xml	Tue Mar 20 22:18:51 2018 -0400
@@ -7,21 +7,21 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        #for $i in $merge.inputs:
-            ln -s "$i" input${merge.inputs.index($i)}.dat &&
-        #end for
+## create symlinks to input datasets
+#for $i in $merge.inputs:
+    ln -s '$i' input${merge.inputs.index($i)}.dat &&
+#end for
 
-        echo 'merge.files(
-            input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#,
-            output=$output
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | sed 's/-,/,/g'
-        | mothur
-        | tee mothur.out.log
+echo 'merge.files(
+    input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#,
+    output=$output
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| sed 's/-,/,/g'
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
     <conditional name="merge">
@@ -48,6 +48,7 @@
             <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/>
         </when> <!-- fasta -->
     </conditional> <!-- merge -->
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -58,10 +59,11 @@
             <param name="type" value="fasta"/>
             <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/>
             <output name="output" file="output.fa" ftype="fasta"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
@@ -71,6 +73,6 @@
 .. _merge.files: https://www.mothur.org/wiki/Merge.files
 
 
-    </help>
-     <expand macro="citations"/>
+    ]]></help>
+    <expand macro="citations"/>
 </tool>