Mercurial > repos > mvdbeek > bam_readtagger
view write_supplementary_fastq.xml @ 43:6f9b1b81b593 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 7ee4c1dd4e13a4d634b0e80efdd2309289a29a1c
author | mvdbeek |
---|---|
date | Fri, 26 Oct 2018 06:11:17 -0400 |
parents | 4fdf606153df |
children | 4870f1d6f037 |
line wrap: on
line source
<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.12"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> <requirement type="package" version="0.4.12">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>