# HG changeset patch
# User dfornika
# Date 1576089710 0
# Node ID 82e55a18143464c2b2246cc4ecf95d99cf808f43
# Parent  1e4197d25ef6ebff10ed19724ea85a0625daab39
"planemo upload for repository https://github.com/phac-nml/mob-suite commit e7f174176bcd08b8b4abce84e12262c840bc0db2-dirty"

diff -r 1e4197d25ef6 -r 82e55a181434 mob_typer.xml
--- a/mob_typer.xml	Wed Dec 11 18:04:06 2019 +0000
+++ b/mob_typer.xml	Wed Dec 11 18:41:50 2019 +0000
@@ -37,12 +37,12 @@
     </section>
   </inputs>
   <outputs>
-    <data name="plasmid_report" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
-      <discover_datasets directory="outdir" pattern="mobtyper.+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
+    <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.name}"  format="tabular" />
+    <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${on_string}: RefSeq Host Range Phylogeny Tree" format="newick">
+      <filter>host_range_detailed</filter>
     </data>
-    <data name="refseq_hostrange_phylogeny_tree" label="${tool.name} on ${on_string}: RefSeq Host Range Phylogeny Tree" format="newick">
-      <discover_datasets directory="outdir" pattern=".+_refseqhostrange_phylogeny_tree\.nwk" format="newick" />
-      <!-- <filter>host_range_detailed</filter> -->
+    <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${tool.name} on ${on_string}: Literature Host Range Phylogeny Tree" format="newick">
+      <filter>host_range_detailed</filter>
     </data>
   </outputs>
   <tests>
@@ -64,6 +64,15 @@
         </assert_contents>
       </output>
     </test>
+    <test>
+      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
+      <param name="host_range_detailed" value="True" />
+      <output name="literature_hostrange_phylogeny_tree">
+        <assert_contents>
+          <has_text text="(90371:1,611:1,28144:1)"/> 
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help>