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Fix HISAT2 strandedness parameter #1470

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merged 12 commits into from
Sep 26, 2017
Merged

Fix HISAT2 strandedness parameter #1470

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9dbc8ef
fix strandedness parameter
mblue9 Sep 8, 2017
823fe2b
add strandedness test and bump version
mblue9 Sep 12, 2017
1dee782
fix indentation
mblue9 Sep 12, 2017
ab9cad1
fix strandness bug, update version and other modifications
mblue9 Sep 17, 2017
619b3b0
remove word accidentally inserted
mblue9 Sep 17, 2017
d4e9996
remove lines accidentally left in
mblue9 Sep 17, 2017
3073d44
fix summary options and add comments back
mblue9 Sep 17, 2017
8e4d6e3
fixes from review
mblue9 Sep 19, 2017
07e9976
small changes to hisat
yhoogstrate Sep 22, 2017
d8a64b9
hisat2 int_quals help fix
yhoogstrate Sep 22, 2017
200afcb
more fixes from feedback
mblue9 Sep 26, 2017
d16f91c
quotes
yhoogstrate Sep 26, 2017
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17 changes: 14 additions & 3 deletions tools/hisat2/hisat2.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="2.0.5.2" profile="17.01">
<tool id="hisat2" name="HISAT2" version="2.0.5.3" profile="17.01">
<description>A fast and sensitive alignment program</description>
<macros>
<import>hisat2_macros.xml</import>
Expand Down Expand Up @@ -464,7 +464,7 @@
<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 -->
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I'd leave the comment here and below, any specific reason to remove them?

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No reason to remove so I put those comments back. I only removed them because they were getting in the way of me commenting out tests while doing my own testing. I just forgot to put them back. I put them back after your review here but then I removed them again for more testing and then forgot to put them back again :( They're back again now.

<test>
<param name="input_format_selector" value="fastq" />
<param name="paired_selector" value="paired" />
<param name="collection_selector" value="files" />
Expand All @@ -480,7 +480,7 @@
<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 -->
<test>
<param name="input_format_selector" value="fastq" />
<param name="paired_selector" value="paired" />
<param name="collection_selector" value="files" />
Expand All @@ -496,6 +496,17 @@
<param name="no_discordant" value="True" />
<output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
</test>
<test>
<param name="input_format_selector" value="fastq" />
<param name="paired_selector" value="paired" />
<param name="collection_selector" value="files" />
<param name="reference_genome_source" value="history" />
<param name="history_item" ftype="fasta" value="phiX.fa" />
<param name="forward" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
<param name="reverse" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
<param name="rna_strandedness" value="F" />
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@nsoranzo nsoranzo Sep 12, 2017 •
edited
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s/rna_strandedness/rna_strandness/
This may actual cause the output bam to be different, I imagine)

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Well this highlighted that my test really was terrible! That strandness parameter was never used because of the typo so my test was checking against a incorrect bam! The lines diff check doesn't catch that but checking the header would, so if there is ever a way in the future to check a bam header that could be cool to help make tests like this one more robust.

<output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" />
</test>
</tests>
<help><![CDATA[
Introduction
Expand Down
10 changes: 9 additions & 1 deletion tools/hisat2/hisat2_macros.xml
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Expand Up @@ -78,7 +78,15 @@
<token name="@strandedness_parameters@">
#if str($spliced_options.spliced_options_selector) == "advanced":
#if str($spliced_options.rna_strandness).strip() != '':
--rna-strandness $spliced_options.rna_strandness
#if str($input_format.paired.paired_selector) == 'paired':
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Indentation.

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Do you use a tool for checking indentation? my eyes don't seem to be very reliable :(

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@mblue9 Unfortunately I'm not aware of tool to check indentation for the Cheetah code inside XML, so basically it's my eyes (on GitHub) or searching for 4 spaces in the text editor.

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@shiltemann shiltemann Sep 20, 2017 •
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@mblue9 no worries, @nsoranzo just has special eagle-eye superpowers the rest of us don't possess ;) 🦅 👀

(but most editors have a setting to show whitespace characters and/or indentation guides, which helps for me)

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Ok, thanks for the tips!

#if str($spliced_options.rna_strandness) == 'F':
--rna-strandness FR
#else:
--rna-strandness RF
#end if
#else:
--rna-strandness $spliced_options.rna_strandness
#end if
#end if
#end if
</token>
Expand Down
Binary file added tools/hisat2/test-data/hisat_output_4.bam
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