comparison hisat2.xml @ 30:6c19daec423d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"

29:26371a1df031

<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy7" profile="17.01">
    <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="1.3">seqtk</requirement>
    </requirements>
    <stdio>
        <regex level="fatal" match="hisat2-align exited with value 1" source="both" />
        <regex level="fatal" match="hisat2: not found" source="both" />
        <exit_code range="1:" />
    </stdio>
    <version_command>hisat2 --version</version_command>
    <command><![CDATA[
## Prepare HISAT2 index

#if $reference_genome.source == "history":
    ln -s '$reference_genome.history_item' genome.fa &&
    hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome &&

        #set read2 = "input_r.fastq"
    #end if
    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} &&
    #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
    #end if
#else:
    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
        #set read1 = "input_f.fastq.gz"
        #set compressed = "GZ"

## - once hisat is finished sort will start to merge the temporary
##   files (which should be fast also on a single thread) gives the
##   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}'

## Rename any output fastq files

#if $output_unaligned_reads_l and $output_unaligned_reads_r:
    #from os.path import splitext

30:6c19daec423d

<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="@TOOL_VERSION@">hisat2</requirement>
        <requirement type="package" version="1.12">samtools</requirement>
        <requirement type="package" version="1.3">seqtk</requirement>
    </requirements>
    <stdio>
        <regex level="fatal" match="hisat2-align exited with value 1" source="both" />
        <regex level="fatal" match="hisat2: not found" source="both" />
        <exit_code range="1:" />
    </stdio>
    <version_command>hisat2 --version</version_command>
    <command><![CDATA[
set -o pipefail;    
## Prepare HISAT2 index

#if $reference_genome.source == "history":
    ln -s '$reference_genome.history_item' genome.fa &&
    hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome &&

        #set read2 = "input_r.fastq"
    #end if
    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 compressed = "GZ"
    #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
        #set compressed = "BZ2"
    #elif $library.input_1.is_of_type('fasta'):
        #set reads_are_fastq = False
    #end if
    #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 $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
        bzcat '${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"):
        #set read1 = "input_f.fastq.gz"
        #set compressed = "GZ"

## - once hisat is finished sort will start to merge the temporary
##   files (which should be fast also on a single thread) gives the
##   sorted output to view which only compresses the files (now
##   using full parallelism again)

| 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

#if $output_unaligned_reads_l and $output_unaligned_reads_r:
    #from os.path import splitext