Mercurial > repos > mvdbeek > bam_readtagger
comparison allow_dovetailing.xml @ 3:cb9036583afe draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
author | mvdbeek |
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date | Tue, 21 Feb 2017 04:39:31 -0500 |
parents | 39d9bc17ec74 |
children | 7625c594bc37 |
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2:39d9bc17ec74 | 3:cb9036583afe |
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1 <tool id="allow_dovetailing" name="Allow dovetailing" version="0.1.13"> | 1 <tool id="allow_dovetailing" name="Allow dovetailing" version="0.2.0"> |
2 <description>modifies proper_pair flag in bam files</description> | 2 <description>modifies proper_pair flag in bam files</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.1.13">readtagger</requirement> | 4 <requirement type="package" version="0.2.0">readtagger</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="aggressive"><![CDATA[ | 6 <command detect_errors="aggressive"><![CDATA[ |
7 allow_dovetailing -i '$input' -o '$output' | 7 allow_dovetailing -i '$input' -o '$output' |
8 ]]></command> | 8 ]]></command> |
9 <inputs> | 9 <inputs> |
17 <param name="input" value="not_a_proper_pair.bam" ftype="bam"/> | 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"/> | 18 <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="2"/> |
19 </test> | 19 </test> |
20 </tests> | 20 </tests> |
21 <help><![CDATA[ | 21 <help><![CDATA[ |
22 :: | 22 .. code-block:: |
23 usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH | |
24 | 23 |
25 Allow dovetailing. | 24 usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH |
26 | 25 |
27 optional arguments: | 26 Allow dovetailing. |
28 -h, --help show this help message and exit | 27 |
29 -i INPUT_PATH, --input_path INPUT_PATH | 28 optional arguments: |
30 Input alignment file to manipulate | 29 -h, --help show this help message and exit |
31 -o OUTPUT_PATH, --output_path OUTPUT_PATH | 30 -i INPUT_PATH, --input_path INPUT_PATH |
32 Output alignment file | 31 Input alignment file to manipulate |
32 -o OUTPUT_PATH, --output_path OUTPUT_PATH | |
33 Output alignment file | |
33 ]]></help> | 34 ]]></help> |
34 </tool> | 35 </tool> |