From 552ba7f9ad84e3fa973c900ef58f846fa9f7bd3f Mon Sep 17 00:00:00 2001
From: Maria Doyle <maria.doyle@petermac.org>
Date: Fri, 29 Sep 2017 20:28:02 +1000
Subject: [PATCH 1/2] fix extra file outputs

---
 tools/hisat2/hisat2.xml | 38 ++++++++++++++++++++++----------------
 1 file changed, 22 insertions(+), 16 deletions(-)

diff --git a/tools/hisat2/hisat2.xml b/tools/hisat2/hisat2.xml
index da571dabe1a..c0c76e51c0e 100644
--- a/tools/hisat2/hisat2.xml
+++ b/tools/hisat2/hisat2.xml
@@ -290,12 +290,10 @@ hisat2
     --summary-file summary.txt
 #end if
 
-
 ## Convert SAM output to sorted BAM
 
 | samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}'
 
-
 ## Rename any output fastq files
 
 #if $output_unaligned_reads_l and $output_unaligned_reads_r:
@@ -540,12 +538,12 @@ hisat2
 
         <!-- Unaligned fastq (L) -->
         <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)">
-            <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True)</filter>
+            <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter>
         </data>
 
         <!-- Aligned fastq (L) -->
         <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)">
-            <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True)</filter>
+            <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter>
         </data>
 
         <!-- Unaligned fastq (R) -->
@@ -567,8 +565,8 @@ hisat2
 
     <!-- Define tests -->
 
-    <tests>
-        <test><!-- Ensure bam output works -->
+    <tests><!-- Ensure bam output works -->
+        <test expect_num_outputs="1" >
             <param name="type" value="paired" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
@@ -576,14 +574,16 @@ hisat2
             <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>
-        <test><!-- Ensure built-in reference works -->
+        <!-- Ensure built-in reference works -->
+        <test expect_num_outputs="1">
             <param name="type" value="paired" />
             <param name="source" value="indexed" />
             <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" />
             <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" />
             <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
         </test>
-        <test><!-- Ensure trimming works -->
+        <!-- Ensure trimming works -->
+        <test expect_num_outputs="1">
             <param name="type" value="paired" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
@@ -594,7 +594,8 @@ hisat2
             <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
             <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" />
         </test>
-        <test><!-- Ensure paired options works -->
+        <!-- Ensure paired options works -->
+        <test expect_num_outputs="1">
             <param name="type" value="paired" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
@@ -608,18 +609,19 @@ hisat2
             <param name="no_discordant" value="True" />
             <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
         </test>
-        <test><!-- Ensure unaligned output works -->
+        <!-- Ensure single unaligned output works -->
+        <test expect_num_outputs="2">
             <param name="type" value="single" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="output_options_selector" value="advanced" />
             <param name="unaligned_file" value="true" />
-            <param name="aligned_file" value="true" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" />
             <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
         </test>
-        <test><!-- Ensure paired unaligned output works -->
+        <!-- Ensure paired unaligned/aligned output works -->
+        <test expect_num_outputs="5">
             <param name="type" value="paired" />
             <param name="source" value="history" />
             <param name="output_options_selector" value="advanced" />
@@ -631,7 +633,8 @@ hisat2
             <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
             <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />
         </test>
-        <test><!-- Ensure fastqsanger.gz works -->
+        <!-- Ensure fastqsanger.gz works -->
+        <test expect_num_outputs="1">
             <param name="type" value="paired" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
@@ -645,7 +648,8 @@ hisat2
             <param name="no_discordant" value="True" />
             <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
         </test>
-        <test><!-- Ensure fastqsanger.bz2 works -->
+        <!-- Ensure fastqsanger.bz2 works -->
+        <test expect_num_outputs="1">
             <param name="type" value="paired" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
@@ -659,7 +663,8 @@ hisat2
             <param name="no_discordant" value="True" />
             <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
         </test>
-        <test><!-- Ensure paired strandness works -->
+        <!-- Ensure paired strandness works -->
+        <test expect_num_outputs="1">
             <param name="type" value="paired" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
@@ -668,7 +673,8 @@ hisat2
             <param name="rna_strandness" value="FR" />
             <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" />
         </test>
-        <test><!-- Ensure summary file output works -->
+        <!-- Ensure summary file output works -->
+        <test expect_num_outputs="2">
             <param name="type" value="single" />
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />

From 8046fcc3b4022b9677015bdbc23a49151190bb51 Mon Sep 17 00:00:00 2001
From: Maria Doyle <maria.doyle@petermac.org>
Date: Sat, 30 Sep 2017 08:53:09 +1000
Subject: [PATCH 2/2] fix from review

---
 tools/hisat2/hisat2.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/hisat2/hisat2.xml b/tools/hisat2/hisat2.xml
index c0c76e51c0e..712e05e1312 100644
--- a/tools/hisat2/hisat2.xml
+++ b/tools/hisat2/hisat2.xml
@@ -565,7 +565,8 @@ hisat2
 
     <!-- Define tests -->
 
-    <tests><!-- Ensure bam output works -->
+    <tests>
+        <!-- Ensure bam output works -->
         <test expect_num_outputs="1" >
             <param name="type" value="paired" />
             <param name="source" value="history" />