Mercurial > repos > mvdbeek > bam_readtagger
view allow_dovetailing.xml @ 61:210427d5c65a draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
author | mvdbeek |
---|---|
date | Sat, 31 Aug 2019 07:19:00 -0400 |
parents | 01acf62d5012 |
children | 16eba798cbc6 |
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<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.8"> <description>modifies proper_pair flag in bam files</description> <requirements> <requirement type="package" version="0.5.8">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' ]]></command> <inputs> <param name="input" argument="--input_path" type="data" format="bam"/> </inputs> <outputs> <data name="output" format="bam"/> </outputs> <tests> <test> <param name="input" value="not_a_proper_pair.bam" ftype="bam"/> <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help><![CDATA[ .. code-block:: usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH Allow dovetailing. optional arguments: -h, --help show this help message and exit -i INPUT_PATH, --input_path INPUT_PATH Input alignment file to manipulate -o OUTPUT_PATH, --output_path OUTPUT_PATH Output alignment file ]]></help> </tool>