# HG changeset patch
# User dfornika
# Date 1573020536 18000
# Node ID faf74a1bbd5faa2071dba21b1973b743a42b9306
# Parent  3616b6eda1dab84e45446e38dc7d4340dedfb7ea
"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"

diff -r 3616b6eda1da -r faf74a1bbd5f match_plasmid_to_reference.xml
--- a/match_plasmid_to_reference.xml	Wed Nov 06 00:42:05 2019 -0500
+++ b/match_plasmid_to_reference.xml	Wed Nov 06 01:08:56 2019 -0500
@@ -9,7 +9,7 @@
         #for $reference_plasmid in $reference_plasmids:
           '${reference_plasmid}'
         #end for
-        --concatenated_mob_typer_reports '${concatenated_mob_typer_reports}'
+        --mob_typer_report '${concatenated_mob_typer_reports}'
         --outdir outdir
     ]]></command>
     <inputs>
@@ -18,7 +18,7 @@
         <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
     </inputs>
     <outputs>
-        <data name="plasmid" from_work_dir="outdir/plasmid.fasta" />
+        <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" />
         <data name="matched_reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" />
 	<data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" />
     </outputs>
@@ -27,14 +27,14 @@
             <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
             <param name="reference_plasmids">
                 <collection type="list">
-                    <element name="CP008719.gbk" value="CP008719.gbk" ftype="genbank" />
-                    <element name="CP008719.gbk" value="CP008719.gbk" ftype="genbank" />
+                    <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
+                    <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
                 </collection>
             </param>
-	    <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
-            <output name="plasmid" file="outdir/plasmid.fasta" />
-            <output name="reference_plasmid" file="outdir/reference_plasmid.gbk" />
-            <output name="mob_typer_record" file="outdir/mob_typer_record.gbk" />
+            <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
+            <output name="output_plasmid" file="outdir/plasmid.fasta" />
+            <output name="matched_reference_plasmid" file="outdir/reference_plasmid.gbk" />
+            <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
         </test>
     </tests>
     <help><![CDATA[