Mercurial > repos > iuc > bioext_bealign
changeset 4:a287431cdf4f draft
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit c9002fa57e4d800f2c1c8d1dafbceb7681b0fcc2"
| author | iuc |
|---|---|
| date | Tue, 05 Oct 2021 09:52:56 +0000 |
| parents | fb4975b507c6 |
| children | c239e93d9f04 |
| files | bealign.xml test-data/bealign-out3-background.bam test-data/bealign_selection.loc |
| diffstat | 3 files changed, 30 insertions(+), 21 deletions(-) [+] |
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--- a/bealign.xml Fri Aug 20 21:04:17 2021 +0000 +++ b/bealign.xml Tue Oct 05 09:52:56 2021 +0000 @@ -3,10 +3,11 @@ <description>to a reference using a codon alignment algorithm</description> <macros> <import>macros.xml</import> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <expand macro="requirements"> <requirement type="package" version="5.1.0">gawk</requirement> + <requirement type="package" version="1.13">samtools</requirement> </expand> <version_command>bealign --version</version_command> <command detect_errors="exit_code"> @@ -18,8 +19,10 @@ ## and replace any unwanted characters in the sequence names with underscores. ## This should not affect the actual alignment, since any non-standard character ## in the sequences is already ignored, but the possibility remains. + set -o pipefail; cat '$input' @SANITIZE@ reads.fa && - bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet + ## bealign's parallel job executor uses the NCPU env variable + NCPU=\${GALAXY_SLOTS:-2} bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet #if $advanced.expected_identity: --expected-identity $advanced.expected_identity #end if @@ -29,26 +32,32 @@ --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference - reads.fa '$output' - #set $input_background = False - #if $background_source.selection == 'history': - #if $background_source.sequences: - #set $input_background = $background_source.sequences - #end if - #else: - #if $background_source.sequences: - #set $input_background = $background_source.sequences.fields.path - #end if + ## bypass bealign's internal pysam-based, single-threaded BAM sorting + --no-sort + reads.fa bealign_out.bam && + samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' bealign_out.bam + #set $input_background = False + #if $background_source.selection == 'history': + #if $background_source.sequences: + #set $input_background = $background_source.sequences + #end if + #else: + #if $background_source.sequences: + #set $input_background = $background_source.sequences.fields.path #end if - #if $input_background: - && cat '$input_background' @SANITIZE@ background.fa && - bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet - #if $advanced.expected_identity: - --expected-identity $advanced.expected_identity - #end if - --keep-reference --score-matrix $advanced.score_matrix $advanced.reverse_complement - background.fa '$background' + #end if + #if $input_background: + && cat '$input_background' @SANITIZE@ background.fa && + NCPU=\${GALAXY_SLOTS:-2} bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet + #if $advanced.expected_identity: + --expected-identity $advanced.expected_identity #end if + --keep-reference --score-matrix $advanced.score_matrix $advanced.reverse_complement + ## bypass bealign's internal pysam-based, single-threaded BAM sorting + --no-sort + background.fa bealign_background.bam && + samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$background' bealign_background.bam + #end if #set $reference_name = str($select_reference.reference) #if $select_reference.reference_type == 'preset' and $select_reference.save_reference: && python '$__tool_directory__/copy_reference.py' --reference '$reference_name' --dataset '$saved_reference'