Mercurial > repos > mvdbeek > bam_readtagger
comparison allow_dovetailing.xml @ 0:a38447a59412 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 17 Feb 2017 10:54:47 -0500 |
| parents | |
| children | f69131f584e8 |
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| -1:000000000000 | 0:a38447a59412 |
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| 1 <tool id="allow_dovetailing" name="Allow dovetailing" version="0.1.8"> | |
| 2 <description>modifies proper_pair flag in bam files</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.1.8">readtagger</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="aggressive"><![CDATA[ | |
| 7 allow_dovetailing -i '$input' -o '$output' | |
| 8 ]]></command> | |
| 9 <inputs> | |
| 10 <param name="input" argument="--input_path" type="data" format="bam"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data name="output" format="bam"/> | |
| 14 </outputs> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="input" value="not_a_proper_pair.bam" ftype="bam"/> | |
| 18 <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="2"/> | |
| 19 </test> | |
| 20 </tests> | |
| 21 <help><![CDATA[ | |
| 22 :: | |
| 23 usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH | |
| 24 | |
| 25 Allow dovetailing. | |
| 26 | |
| 27 optional arguments: | |
| 28 -h, --help show this help message and exit | |
| 29 -i INPUT_PATH, --input_path INPUT_PATH | |
| 30 Input alignment file to manipulate | |
| 31 -o OUTPUT_PATH, --output_path OUTPUT_PATH | |
| 32 Output alignment file | |
| 33 ]]></help> | |
| 34 </tool> |