Mercurial > repos > mvdbeek > bam_readtagger
view allow_dovetailing.xml @ 7:d2009cdcdeba draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2d4b104e1209152cc6c2c7e99c3035ff1f23ce9e-dirty
author | mvdbeek |
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date | Fri, 03 Mar 2017 10:30:14 -0500 |
parents | 50471302eb73 |
children | bf8ffb337cbe |
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<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.3"> <description>modifies proper_pair flag in bam files</description> <requirements> <requirement type="package" version="0.3.3">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="2"/> </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>