Mercurial > repos > artbio > mapping_quality_stats
comparison mapping_quality_stats.xml @ 0:f00479673d47 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
| author | artbio |
|---|---|
| date | Wed, 15 Jun 2022 10:43:07 +0000 |
| parents | |
| children | 7883d97fa479 |
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| -1:000000000000 | 0:f00479673d47 |
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| 1 <tool id="mapqstatistics" name="Mapping Quality Stats" version="0.16.0.1+galaxy0"> | |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement> | |
| 5 <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement> | |
| 6 <requirement type="package" version="0.16.0.1">pysam</requirement> | |
| 7 </requirements> | |
| 8 <stdio> | |
| 9 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 10 </stdio> | |
| 11 <command detect_errors="exit_code"><![CDATA[ | |
| 12 ln -f -s $input.metadata.bam_index input.bam.bai && | |
| 13 ln -s $input input.bam && | |
| 14 python $__tool_directory__/mapping_quality_stats.py | |
| 15 -bam input.bam | |
| 16 -o $table && | |
| 17 Rscript $__tool_directory__/mapping_quality_stats.r | |
| 18 -i '$table' | |
| 19 -o $plot | |
| 20 ]]></command> | |
| 21 <inputs> | |
| 22 <param name="input" type="data" format="bam" label="Select a bam file to analyze"/> | |
| 23 </inputs> | |
| 24 | |
| 25 <outputs> | |
| 26 <data format="tabular" name="table" label="Distribution table" /> | |
| 27 <data format="pdf" name="plot" label="Distribution of MAPQs" /> | |
| 28 </outputs> | |
| 29 | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input" value="sample.bam" ftype="bam"/> | |
| 33 <output file="distribution.tab" name="table" /> | |
| 34 <output file="distribution.pdf" name="plot" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 | |
| 38 | |
| 39 <help> | |
| 40 | |
| 41 **What it does** | |
| 42 | |
| 43 Collects the values of mapping quality (MAPQ) in a BAM files | |
| 44 Shows the data as a table and a barplot | |
| 45 | |
| 46 **Inputs** | |
| 47 | |
| 48 A bam alignment files which must be sorted | |
| 49 | |
| 50 **Output** | |
| 51 | |
| 52 A data frame of MAPQ counts | |
| 53 | |
| 54 A pdf barplot generated by R and ggplot2 | |
| 55 | |
| 56 </help> | |
| 57 | |
| 58 <citations> | |
| 59 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
| 60 </citations> | |
| 61 </tool> | |
| 62 |