# HG changeset patch
# User rnateam
# Date 1654593585 0
# Node ID 74b0ca4446af5d4613030b1529f3d930a97dd1ea
# Parent  579b3be2559fa74de0aa0b392773cf457dc33a86
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 07674fe3507909d11d7431e3b8c48afcfb1f4b5e"

diff -r 579b3be2559f -r 74b0ca4446af ribotaper_part1_create_annotation_files.xml
--- a/ribotaper_part1_create_annotation_files.xml	Fri Jun 03 20:17:28 2022 +0000
+++ b/ribotaper_part1_create_annotation_files.xml	Tue Jun 07 09:19:45 2022 +0000
@@ -10,12 +10,12 @@
     <command><![CDATA[
         #if $reference_genome.source == 'history':
             #set $ref_genome = 'reference.fasta'
-            ln -s -f '${reference_genome.history_item}' $ref_genome
-            && samtools faidx $ref_genome
+            ln -s -f '${reference_genome.history_item}' $ref_genome &&
+            samtools faidx $ref_genome &&
         #else:
             #set $ref_genome = $reference_genome.index.fields.path
         #end if
-        && create_annotations_files.bash
+        create_annotations_files.bash
         '${gtf}'
         '${ref_genome}'
         $ccdsid
@@ -67,6 +67,16 @@
             <param name="appris" value="true"/>
             <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
         </test>
+        <test expect_num_outputs="2">
+            <param name="gtf" value="test.gtf"/>
+            <conditional name="reference_genome">
+                <param name="source" value="indexed"/>
+                <param name="index" value="phix174"/>
+            </conditional>
+            <param name="ccdsid" value="true"/>
+            <param name="appris" value="true"/>
+            <output name="output1" file="annotation_path/start_stops_FAR_indexed.bed"/>
+        </test>
     </tests>
     <help><![CDATA[
 Overview
diff -r 579b3be2559f -r 74b0ca4446af test-data/annotation_path/start_stops_FAR_indexed.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation_path/start_stops_FAR_indexed.bed	Tue Jun 07 09:19:45 2022 +0000
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