comparison minimap2.xml @ 1:b103bc946f57 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739

0:2445d53549ba

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="2.3" profile="17.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <requirements>
        <requirement type="package" version="2.3">minimap2</requirement>
        <requirement type="package" version="1.6">samtools</requirement>
    </requirements>
    <version_command>minimap2 --version</version_command>
    <command>
<![CDATA[

minimap2 may align ~1% of read bases with long CIGARs beyond the
capability of BAM. If you convert such SAM/CRAM to BAM, Picard and
recent samtools will throw an error and abort. Older samtools and other
tools may create corrupted BAM.

To avoid this issue, you can add option ``-L`` at the minimap2 command
line. This option moves a long CIGAR to the ``CG`` tag and leaves a
fully clipped CIGAR at the SAM CIGAR column. Current tools that don’t
read CIGAR (e.g. merging and sorting) still work with such BAM records;
tools that read CIGAR will effectively ignore these records. I have pull
requests to the SAM spec, htslib, htsjdk, bedtools2, Rsamtools and
igv.js. If they are accepted, future versions of these tools will
seamlessly recognize long-cigar records generated by option ``-L``.

**TD;DR**: if you work with ultra-long reads and use tools that only
process BAM files, please add option ``-L``.

The cs optional tag

1:b103bc946f57

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="2.4" profile="17.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <requirements>
        <requirement type="package" version="2.4">minimap2</requirement>
        <requirement type="package" version="1.6">samtools</requirement>
    </requirements>
    <version_command>minimap2 --version</version_command>
    <command>
<![CDATA[

minimap2 may align ~1% of read bases with long CIGARs beyond the
capability of BAM. If you convert such SAM/CRAM to BAM, Picard and
recent samtools will throw an error and abort. Older samtools and other
tools may create corrupted BAM.

To avoid this issue, you can add option ``-L`` at the minimap2 command line.
This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped
CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR
(e.g. merging and sorting) still work with such BAM records; tools that read
CIGAR will effectively ignore these records. It has been decided that future
tools will seamlessly recognize long-cigar records generated by option `-L`.

**TD;DR**: if you work with ultra-long reads and use tools that only
process BAM files, please add option ``-L``.

The cs optional tag