Mercurial > repos > mvdbeek > size_distribution
comparison alignment_size_distribution.xml @ 0:ac5584567084 draft
planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
| author | mvdbeek |
|---|---|
| date | Mon, 20 Aug 2018 12:39:15 -0400 |
| parents | |
| children | 3ed18dcb6f82 |
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| -1:000000000000 | 0:ac5584567084 |
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| 1 <tool id="alignment_size_distribution" name="Create size distribution for alignment files" version="0.1.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="6.7">click</requirement> | |
| 4 <requirement type="package" version="0.23">pandas</requirement> | |
| 5 <requirement type="package" version="0.15">pysam</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 python '/size_distributions.py' '$alignment_file' --minimum_size $minimum_size --maximum_size $maximum_size $wide --output '$distribution' | |
| 9 ]]></command> | |
| 10 <inputs> | |
| 11 <param name="alignment_file" type="data" format="bam,unsorted.bam"/> | |
| 12 <param argument="--minimum_size" type="integer" value="18" min="1" label="Minimum read length to consider"/> | |
| 13 <param argument="--maximum_size" type="integer" value="18" min="1" label="Maximum read length to consider"/> | |
| 14 <param argument="--wide" type="boolean" checked="false" truevalue="--wide" label="Output wide instead of long tabular format"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data name="distribution" format="tabular"/> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="alignment_file" value="test_data.bam" ftype="bam"/> | |
| 22 <output name="distribution" value="distribution.tab" ftype="tabular"/> | |
| 23 </test> | |
| 24 </tests> | |
| 25 <help><![CDATA[ | |
| 26 Generates a table with reference sequence, sense and antisense counts. | |
| 27 ]]></help> | |
| 28 </tool> |