comparison hisat2.xml @ 21:0b1c04a90182 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit dac38d1735c11fe614d0a986a796e33eb7f4a469

20:6ab42baa56e9

<tool id="hisat2" name="HISAT2" version="2.1.0" 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="1.4">samtools</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[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && 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 &&

#if str($sum.summary_file) == "true":
    --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:
    #from os.path import splitext

21:0b1c04a90182

<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy1" 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="1.8">samtools</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 &&

#if str($sum.summary_file) == "true":
    --summary-file summary.txt
#end if

## Convert SAM output to sorted BAM
## using the two pipe stages has the following effect
## - hisat2 and sort run in parallel, during this time sort produces
##   presorted temporary files but does not produce output (hence 
##   view does not run)
## - 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 -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