# HG changeset patch
# User earlhaminst
# Date 1623002132 0
# Node ID 692832801d70d470670c39274215e493fab3ffb8
# Parent  fc78d02657a98f232e52940648d71a204cb056f9
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c"

diff -r fc78d02657a9 -r 692832801d70 lotus2.xml
--- a/lotus2.xml	Sat Jun 05 09:49:25 2021 +0000
+++ b/lotus2.xml	Sun Jun 06 17:55:32 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">
+<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.01">
     <description>fast OTU processing pipeline</description>
     <macros>
         <token name="@VERSION@">2.07</token>
@@ -179,7 +179,7 @@
 
 ; EXIT_VALUE=\$? ;
 
-tar -cvzf output.tar.gz output/
+zip -8 -r -v output.zip output/
 &&
 exit \$EXIT_VALUE
     ]]></command>
@@ -329,13 +329,12 @@
     </inputs>
 
     <outputs>
+        <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
         <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
-        <data name="otu_biom" format="biom1" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" />
         <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
         <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
         <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
         <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />
-        <data name="outputs" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" />
     </outputs>
 
     <tests>