# HG changeset patch
# User iuc
# Date 1522099415 14400
# Node ID 3c3d8f1e7804bae22680fa38583220b2b06057fe
# Parent  6f718d3182d7f2d644a648df4b19aaf912f9708c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940

diff -r 6f718d3182d7 -r 3c3d8f1e7804 hisat2.xml
--- a/hisat2.xml	Tue Nov 14 05:28:32 2017 -0500
+++ b/hisat2.xml	Mon Mar 26 17:23:35 2018 -0400
@@ -233,8 +233,8 @@
     --np ${adv.scoring_options.ambiguous_penalty}
     --rdg ${adv.scoring_options.read_open_penalty},${adv.scoring_options.read_extend_penalty}
     --rfg ${adv.scoring_options.ref_open_penalty},${adv.scoring_options.ref_extend_penalty}
-    --sp ${scoring_options.soft_clip_penalty_max},${adv.scoring_options.soft_clip_penalty_min}
-    --score-min ${scoring_options.function_type},${adv.scoring_options.constant_term},${adv.scoring_options.coefficient}
+    --sp ${adv.scoring_options.soft_clip_penalty_max},${adv.scoring_options.soft_clip_penalty_min}
+    --score-min ${adv.scoring_options.function_type},${adv.scoring_options.constant_term},${adv.scoring_options.coefficient}
 #end if
 
 
@@ -575,6 +575,16 @@
             <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
             <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
         </test>
+        <!-- Ensure advanced scoring options work -->
+        <test expect_num_outputs="1" >
+            <param name="type" value="paired" />
+            <param name="source" value="history" />
+            <param name="history_item" ftype="fasta" value="phiX.fa" />
+            <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
+            <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
+            <param name="adv|scoring_options|coefficient" value="-0.3"/>
+            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
+        </test>
         <!-- Ensure built-in reference works -->
         <test expect_num_outputs="1">
             <param name="type" value="paired" />