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fix hisat2 extra outputs #1497

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merged 2 commits into from
Sep 30, 2017
Merged

fix hisat2 extra outputs #1497

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552ba7f
fix extra file outputs
mblue9 Sep 29, 2017
8046fcc
fix from review
mblue9 Sep 29, 2017
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38 changes: 22 additions & 16 deletions tools/hisat2/hisat2.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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) -->
Expand All @@ -567,23 +565,25 @@ hisat2

<!-- Define tests -->

<tests>
<test><!-- Ensure bam output works -->
<tests><!-- Ensure bam output works -->
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    <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" />
<param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
<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" />
Expand All @@ -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" />
Expand All @@ -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" />
Expand All @@ -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" />
Expand All @@ -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" />
Expand All @@ -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" />
Expand All @@ -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" />
Expand Down