diff pairwise.seqs.xml @ 3:cc74f42d74a2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4

--- a/pairwise.seqs.xml	Tue Sep 05 16:28:20 2017 -0400
+++ b/pairwise.seqs.xml	Wed Feb 14 09:29:51 2018 -0500
@@ -7,35 +7,35 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
 
-        echo 'pairwise.seqs(
-            fasta=fasta.dat,
-            align=$align,
-            #if $calc:
-                calc=$calc,
-            #end if
-            $countends
-            #if float($cutoff) > 0.0:
-                cutoff=$cutoff,
-            #end if
-            #if $scoring.setby == "user":
-                match=$scoring.match,
-                mismatch=$scoring.mismatch,
-                gapopen=$scoring.gapopen,
-                gapextend=$scoring.gapextend,
-            #end if
-            #if $output:
-                output=$output,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'pairwise.seqs(
+    fasta=fasta.dat,
+    align=$align,
+    #if $calc:
+        calc=$calc,
+    #end if
+    $countends
+    #if float($cutoff) > 0.0:
+        cutoff=$cutoff,
+    #end if
+    #if $scoring.setby == "user":
+        match=$scoring.match,
+        mismatch=$scoring.mismatch,
+        gapopen=$scoring.gapopen,
+        gapextend=$scoring.gapextend,
+    #end if
+    #if $output:
+        output=$output,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
@@ -108,8 +108,7 @@
             <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -123,7 +122,6 @@
 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>