Mercurial > repos > iuc > mothur_degap_seqs

diff degap.seqs.xml @ 2:f643cbd3a967 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:56:13 -0400
parents 7cd72305d496
children
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line diff
--- a/degap.seqs.xml	Tue Sep 05 17:13:48 2017 -0400
+++ b/degap.seqs.xml	Tue Mar 20 21:56:13 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 'degap.seqs(
-            fasta=fasta.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'degap.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" label="fasta - Dataset"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -30,6 +31,7 @@
         <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.ng.fasta"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>