Mercurial > repos > iuc > hisat2
changeset 32:4a826a536dcb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"
| author | iuc |
|---|---|
| date | Sun, 18 Jul 2021 17:50:20 +0000 |
| parents | aac14659f53c |
| children | b140ee457381 |
| files | hisat2.xml hisat2_macros.xml test-data/hisat_output_5.bam test-data/hisat_output_spliced_1.bam |
| diffstat | 4 files changed, 15 insertions(+), 15 deletions(-) [+] |
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--- a/hisat2.xml Mon Jan 25 17:28:43 2021 +0000 +++ b/hisat2.xml Sun Jul 18 17:50:20 2021 +0000 @@ -1,11 +1,11 @@ -<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy7" profile="17.01"> +<tool id="hisat2" name="HISAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> </macros> <requirements> - <requirement type="package" version="2.1.0">hisat2</requirement> - <requirement type="package" version="1.11">samtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">hisat2</requirement> + <requirement type="package" version="1.12">samtools</requirement> <requirement type="package" version="1.3">seqtk</requirement> </requirements> <stdio> @@ -15,6 +15,7 @@ </stdio> <version_command>hisat2 --version</version_command> <command><![CDATA[ +set -o pipefail; ## Prepare HISAT2 index #if $reference_genome.source == "history": @@ -96,24 +97,20 @@ ln -s '${library.input_1.reverse}' ${read2} && #elif str( $library.type ) == "paired_interleaved": #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): - #set interleaved_reads = "input_f.fastq.gz" #set compressed = "GZ" #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set interleaved_reads = "input_f.fastq.bz2" #set compressed = "BZ2" #elif $library.input_1.is_of_type('fasta'): #set reads_are_fastq = False - #set interleaved_reads = "input_f.fasta" - #else: - #set interleaved_reads = "input_f.fastq" #end if - ln -f -s '${library.input_1}' ${interleaved_reads} && + #set read1 = "input_f.fastq" if reads_are_fastq else "input_f.fasta" + #set read2 = "input_r.fastq" if reads_are_fastq else "input_r.fasta" #if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = "<(bzcat input_f.fastq.bz2 | seqtk seq -1 /dev/stdin)" - #set read2 = "<(bzcat input_f.fastq.bz2 | seqtk seq -2 /dev/stdin)" - #else: - #set read1 = "<(seqtk seq -1 %s)" % $interleaved_reads - #set read2 = "<(seqtk seq -2 %s)" % $interleaved_reads + bzcat '${library.input_1}' | seqtk seq -1 /dev/stdin > $read1 && + bzcat '${library.input_1}' | seqtk seq -2 /dev/stdin > $read2 && + #else + seqtk seq -1 '${library.input_1}' > $read1 && + seqtk seq -2 '${library.input_1}' > $read2 && #end if #else: #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): @@ -348,7 +345,7 @@ ## sorted output to view which only compresses the files (now ## using full parallelism again) -| samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' +| samtools sort --no-PG -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' ## Rename any output fastq files
--- a/hisat2_macros.xml Mon Jan 25 17:28:43 2021 +0000 +++ b/hisat2_macros.xml Sun Jul 18 17:50:20 2021 +0000 @@ -1,4 +1,7 @@ <macros> + <token name="@TOOL_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="paired_end_options"> <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"