Mercurial > repos > iuc > qq_manhattan

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"planemo upload commit 3126d8d1bdf88d13a8d168020bdf03dbb2dd1c0b"
author iuc
date Thu, 08 Oct 2020 17:28:43 +0000
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7a8a21c5a57f "planemo upload commit 3126d8d1bdf88d13a8d168020bdf03dbb2dd1c0b"
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1 <tool id="qq_manhattan" name="Manhattan Plots" version="0.1.0" profile="19.05">
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2 <requirements>
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3 <requirement type="package" version="0.1.4">r-qqman</requirement>
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4 <requirement type="package" version="1.6.4">r-optparse</requirement>
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5 </requirements>
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6 <command detect_errors='exit_code'><![CDATA[
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7 Rscript $__tool_directory__/manhattan.R --file '$data' --pval '$pval' --chr '$chr' --bp '$bp' --snp '$snp' --name '$name'
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8 ]]></command>
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9 <inputs>
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10 <param name="data" type="data" format="tabular,tsv" label="Data file"/>
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11 <param name="pval" type="text" value="P" label="P-value column name in input file"/>
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12 <param name="chr" type="text" value="CHR" label="Chromosome column name in input file"/>
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13 <param name="bp" type="text" value="BP" label="Base pair coordinate column name in input file"/>
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14 <param name="snp" type="text" value="SNP" label="SNP ID column name in input file"/>
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15 <param name="name" type="text" value="Manhattan Plot" label="Plot title"/>
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16 </inputs>
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17 <outputs>
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18 <data format="pdf" name="manhattan" from_work_dir="manhattan.pdf"/>
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19 </outputs>
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20 <tests>
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21 <test expect_num_outputs="1">
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22 <param name="data" value="test.tsv"/>
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23 <output name="manhattan" file="manhattan.pdf" compare="sim_size"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 Simple manhattan plot wrapper usinng the qqman bioconductor package.
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28 ]]></help>
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29 <citations>
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30 <citation type="doi">https://doi.org/10.1101/005165</citation>
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31 </citations>
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32 </tool>