# HG changeset patch
# User dfornika
# Date 1570841319 14400
# Node ID 869ab16717dba59b5dc8cc969468b7e7f2264769
# Parent  d21fd5069821b15b5899a1a4a9a4cc1f49ad099f
"planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/uvp commit 2482e856a9414983c82d94c9f59ff8985574895e-dirty"

diff -r d21fd5069821 -r 869ab16717db uvp.xml
--- a/uvp.xml	Fri Oct 11 20:32:46 2019 -0400
+++ b/uvp.xml	Fri Oct 11 20:48:39 2019 -0400
@@ -21,16 +21,16 @@
         uvp
             --threads \${GALAXY_SLOTS:-1}
             #if $single_paired.single_paired_selector == 'yes'
-                -n '${single_paired.forward_input.element_identifier}'
-                -q 'R1.fastq.gz'
-                -q2 'R2.fastq.gz'
+                -n 'sample'
+                -q '${single_paired.forward_input}'
+                -q2 '${single_paired.reverse_input}'
             #elif $single_paired.single_paired_selector == "collection":
-                -n '${single_paired.input_pair.forward.element_identifier}'
-                -q 'R1.fastq.gz'
-                -q2 'R2.fastq.gz'
+                -n 'sample'
+                -q '${single_paired.input_pair.forward}'
+                -q2 '${single_paired.input_pair.reverse}'
             #else:
-                -n '${single_paired.input_sequences.element_identifier}'
-                -q 'R1.fastq.gz'
+                -n 'sample'
+                -q '${single_paired.input_sequences}'
             #end if
             --krakendb '${kraken_database.fields.path}'
             -r '${reference}'
@@ -64,6 +64,7 @@
 	<param name="annotate" type="boolean" truevalue="--annotate" falsevalue="" />
     </inputs>
     <outputs>
+        <data name="lineage_report" label="Lineage Report" format="tabular" from_work_dir="Results/sample/sample.lineage_report.txt"/>
         <data name="low_quals" label="Low-quality" format="tabular" from_work_dir="QC/low_quals.txt"/>
     </outputs>
     <tests>