Mercurial > repos > iuc > qq_manhattan
comparison qq_manhattan.xml @ 0:60695e0c8dbf draft default tip
"planemo upload commit 3126d8d1bdf88d13a8d168020bdf03dbb2dd1c0b"
| author | iuc |
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| date | Thu, 08 Oct 2020 17:27:55 +0000 |
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| -1:000000000000 | 0:60695e0c8dbf |
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| 1 <tool id="qq_manhattan" name="Manhattan Plots" version="0.1.0" profile="19.05"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="0.1.4">r-qqman</requirement> | |
| 4 <requirement type="package" version="1.6.4">r-optparse</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors='exit_code'><![CDATA[ | |
| 7 Rscript $__tool_directory__/manhattan.R --file '$data' --pval '$pval' --chr '$chr' --bp '$bp' --snp '$snp' --name '$name' | |
| 8 ]]></command> | |
| 9 <inputs> | |
| 10 <param name="data" type="data" format="tabular,tsv" label="Data file"/> | |
| 11 <param name="pval" type="text" value="P" label="P-value column name in input file"/> | |
| 12 <param name="chr" type="text" value="CHR" label="Chromosome column name in input file"/> | |
| 13 <param name="bp" type="text" value="BP" label="Base pair coordinate column name in input file"/> | |
| 14 <param name="snp" type="text" value="SNP" label="SNP ID column name in input file"/> | |
| 15 <param name="name" type="text" value="Manhattan Plot" label="Plot title"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="pdf" name="manhattan" from_work_dir="manhattan.pdf"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test expect_num_outputs="1"> | |
| 22 <param name="data" value="test.tsv"/> | |
| 23 <output name="manhattan" file="manhattan.pdf" compare="sim_size"/> | |
| 24 </test> | |
| 25 </tests> | |
| 26 <help><![CDATA[ | |
| 27 Simple manhattan plot wrapper usinng the qqman bioconductor package. | |
| 28 ]]></help> | |
| 29 <citations> | |
| 30 <citation type="doi">https://doi.org/10.1101/005165</citation> | |
| 31 </citations> | |
| 32 </tool> |