Mercurial > repos > mvdbeek > bam_readtagger
view write_supplementary_fastq.xml @ 35:02afdbc69591 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef
author | mvdbeek |
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date | Thu, 14 Dec 2017 03:52:04 -0500 |
parents | 240c901dedc0 |
children | d0b3329a8e4b |
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<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.4"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ write_supplementary_fastq --input_path '$input' --output_path '$output' ]]></command> <inputs> <param name="input" argument="--input_path" type="data" format="bam"/> </inputs> <outputs> <data name="output" format="fastqsanger"/> </outputs> <tests> <test> <param name="input" value="supplementary.bam" ftype="bam"/> <output name="output" file="supplementary.fastq" ftype="fastqsanger"/> </test> </tests> <help><![CDATA[ .. code-block:: Usage: write_supplementary_fastq [OPTIONS] Write all supplementary alignments in `input_path` to an output fastq file at `output_path`. Options: --input_path PATH Collect supplementary reads in this alignment file. --output_path PATH Write supplementary reads to this FASTQ file. --help Show this message and exit. ]]></help> </tool>