Mercurial > repos > mvdbeek > bam_readtagger
view update_mapq.xml @ 52:b03c6d8c37c1 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 45d0337e2a0d35e9a83d9c87c005c876c45ee054
author | mvdbeek |
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date | Wed, 12 Jun 2019 14:23:52 -0400 |
parents | 08656cd6c989 |
children | 5eb0ec276ea5 |
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<tool id="update_mapq" name="Update MAPQ score" version="0.5.0"> <description>of supplementary alignments</description> <requirements> <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path' ]]></command> <inputs> <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/> <param argument="--remapped_path" label="Extract MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/> </inputs> <outputs> <data name="output_path" format="bam"/> </outputs> <tests> <test> <param name="source_path" value="supplementary.bam" ftype="bam"/> <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/> <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/> </test> </tests> <help><![CDATA[ .. code-block:: Usage: update_mapq [OPTIONS] Update supplementary read MAPQ score after remapping. Options: --source_path PATH Alignment file where supplementary reads should be updated with new MAPQ scores [required] --remapped_path PATH Alignment file that contains reads that have been remapped and contain an updated MAPQ score [required] --output_path PATH Write all alignments in original_path to this location. Supplementary reads will take the MAPQ score as determined by remapping to the alignment file at `remapped_path` [required] --version Show the version and exit. --help Show this message and exit. ]]></help> </tool>