# HG changeset patch
# User iuc
# Date 1506760981 14400
# Node ID a537774e1979fb511546deae100c89410943c149
# Parent  f9fe48bdc5dbf70020b56fa8e0fc081ee1a9c171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632

diff -r f9fe48bdc5db -r a537774e1979 hisat2.xml
--- a/hisat2.xml	Tue Sep 26 17:01:57 2017 -0400
+++ b/hisat2.xml	Sat Sep 30 04:43:01 2017 -0400
@@ -290,12 +290,10 @@
     --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 @@
 
         <!-- 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) -->
@@ -568,7 +566,8 @@
     <!-- Define tests -->
 
     <tests>
-        <test><!-- Ensure bam output works -->
+        <!-- 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 +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>
-        <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 +595,8 @@
             <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 +610,19 @@
             <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 +634,8 @@
             <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 +649,8 @@
             <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 +664,8 @@
             <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 +674,8 @@
             <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" />