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"planemo upload commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
author iuc
date Fri, 11 Oct 2019 17:31:09 -0400
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1 <tool id="gwastools_manhattan_plot" name="Manhattan plot" version="0.1.0" python_template_version="3.5">
2 <description>Generate plots for use with GWAS pipelines</description>
3 <requirements>
4 <requirement type="package" version="3.6">r-base</requirement>
5 <requirement type="package" version="1.30.0">bioconductor-gwastools</requirement>
6 <requirement type="package" version="1.6.4">r-optparse</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '$__tool_directory__/manhattan.R'
10 --file '${file}'
11 --pval ${pvals}
12 --chromosome ${chromosome}
13 #if $ymax:
14 --ymax ${ymax}
15 #end if
16 #if $ymin:
17 --ymin ${ymin}
18 #end if
19 ${trunc}
20 #if $sig:
21 --sig ${sig}
22 #end if
23 #if $thinselect.thinning == 'Yes':
24 --thin ${thinselect.thin}
25 #if $thinselect.ppb:
26 --ppb ${thinselect.ppb}
27 #end if
28 #end if
29 ]]></command>
30 <inputs>
31 <param name="file" type="data" format="tsv,tabular" label="GWAS data file"/>
32 <param name="chromosome" type="data_column" data_ref="file" label="Chromosome column number"/>
33 <param name="pvals" type="data_column" data_ref="file" label="P-values column number"/>
34 <param name="ymax" type = "float" optional="true" label="Y max"/>
35 <param name="ymin" type = "float" optional="true" label="Y min"/>
36 <param name="trunc" type="boolean" truevalue="--trunc" falsevalue="" label="Show truncation lines?"/>
37 <param name="sig" type="float" optional="true" label="Genome-wide significance level for plotting horizontal line." help="If not specified, no line will be drawn."/>
38 <conditional name="thinselect">
39 <param name="thinning" type="select" label='Specify thinning value?'>
40 <option value="Yes"/>
41 <option value="No"/>
42 </param>
43 <when value="Yes">
44 <param name="thin" type="float" value="0" label="Threshold for thinning points" help="If not specified, value is -log10(val)"/>
45 <param name="ppb" type="integer" optional="true" label="Points per bin"/>
46 </when>
47 <when value="No"/>
48 </conditional>
49 </inputs>
50 <outputs>
51 <data name="manhattanout" format="pdf" from_work_dir="manhattan.pdf" label="Manhattan plot on ${on_string}"/>
52 </outputs>
53 <tests>
54 <test expect_num_outputs="1">
55 <param name="file" value="sampledata.tsv"/>
56 <param name="chromosome" value="2"/>
57 <param name="pvals" value="4"/>
58 <param name="ymin" value="0.2"/>
59 <param name="trunc" value="--trunc"/>
60 <param name="ymax" value="2"/>
61 <param name="sig" value="0.05"/>
62 <conditional name="thinselect">
63 <param name="thinning" value="yes"/>
64 <param name="thin" value="1"/>
65 <param name="ppb" value="1"/>
66 </conditional>
67 <output name="manhattanout" ftype="pdf" value="testgraph.pdf" compare="sim_size"/>
68 </test>
69 </tests>
70 <help><![CDATA[
71 Generates a manhattan plot for GWAS data
72
73 Input data format example:
74
75 SNP CHR Pos P
76 rs1 1 1 0.9148
77 rs2 1 2 0.9371
78 rs3 1 3 0.2861
79 rs4 1 4 0.8304
80 rs5 1 5 0.6417
81 rs6 1 6 0.5191
82 rs16468 22 533 0.1779
83
84 ]]></help>
85 <citations>
86 <citation type="doi">10.1093/bioinformatics/bts610</citation>
87 </citations>
88 </tool>