diff reverse.seqs.xml @ 2:503898f17f42 draft

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

--- a/reverse.seqs.xml	Tue Sep 05 17:17:59 2017 -0400
+++ b/reverse.seqs.xml	Tue Mar 20 21:55:28 2018 -0400
@@ -7,20 +7,21 @@
     <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 'reverse.seqs(
-            fasta=fasta.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'reverse.seqs(
+    fasta=fasta.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -30,11 +31,11 @@
         <test>
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
             <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -43,7 +44,7 @@
 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.
 
 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>