Mercurial > repos > iuc > gwastools_manhattan_plot

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"planemo upload commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:37:42 +0000
parents 86b0ee02918a
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1 <tool id="gwastools_manhattan_plot" name="Manhattan plot" version="0.1.0" python_template_version="3.5">
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2 <description>Generate plots for use with GWAS pipelines</description>
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3 <xrefs>
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4 <xref type="bio.tools">gwastools</xref>
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5 </xrefs>
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6 <requirements>
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7 <requirement type="package" version="3.6">r-base</requirement>
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8 <requirement type="package" version="1.30.0">bioconductor-gwastools</requirement>
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9 <requirement type="package" version="1.6.4">r-optparse</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 Rscript '$__tool_directory__/manhattan.R'
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13 --file '${file}'
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14 --pval ${pvals}
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15 --chromosome ${chromosome}
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16 #if $ymax:
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17 --ymax ${ymax}
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18 #end if
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19 #if $ymin:
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20 --ymin ${ymin}
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21 #end if
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22 ${trunc}
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23 #if $sig:
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24 --sig ${sig}
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25 #end if
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26 #if $thinselect.thinning == 'Yes':
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27 --thin ${thinselect.thin}
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28 #if $thinselect.ppb:
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29 --ppb ${thinselect.ppb}
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30 #end if
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31 #end if
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32 ]]></command>
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33 <inputs>
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34 <param name="file" type="data" format="tsv,tabular" label="GWAS data file"/>
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35 <param name="chromosome" type="data_column" data_ref="file" label="Chromosome column number"/>
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36 <param name="pvals" type="data_column" data_ref="file" label="P-values column number"/>
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37 <param name="ymax" type = "float" optional="true" label="Y max"/>
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38 <param name="ymin" type = "float" optional="true" label="Y min"/>
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39 <param name="trunc" type="boolean" truevalue="--trunc" falsevalue="" label="Show truncation lines?"/>
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40 <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."/>
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41 <conditional name="thinselect">
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42 <param name="thinning" type="select" label='Specify thinning value?'>
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43 <option value="Yes"/>
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44 <option value="No"/>
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45 </param>
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46 <when value="Yes">
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47 <param name="thin" type="float" value="0" label="Threshold for thinning points" help="If not specified, value is -log10(val)"/>
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48 <param name="ppb" type="integer" optional="true" label="Points per bin"/>
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49 </when>
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50 <when value="No"/>
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51 </conditional>
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52 </inputs>
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53 <outputs>
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54 <data name="manhattanout" format="pdf" from_work_dir="manhattan.pdf" label="Manhattan plot on ${on_string}"/>
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55 </outputs>
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56 <tests>
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57 <test expect_num_outputs="1">
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58 <param name="file" value="sampledata.tsv"/>
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59 <param name="chromosome" value="2"/>
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60 <param name="pvals" value="4"/>
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61 <param name="ymin" value="0.2"/>
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62 <param name="trunc" value="--trunc"/>
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63 <param name="ymax" value="2"/>
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64 <param name="sig" value="0.05"/>
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65 <conditional name="thinselect">
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66 <param name="thinning" value="yes"/>
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67 <param name="thin" value="1"/>
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68 <param name="ppb" value="1"/>
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69 </conditional>
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70 <output name="manhattanout" ftype="pdf" value="testgraph.pdf" compare="sim_size"/>
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 Generates a manhattan plot for GWAS data
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75
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76 Input data format example:
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77
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78 SNP CHR Pos P
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79 rs1 1 1 0.9148
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80 rs2 1 2 0.9371
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81 rs3 1 3 0.2861
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82 rs4 1 4 0.8304
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83 rs5 1 5 0.6417
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84 rs6 1 6 0.5191
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85 rs16468 22 533 0.1779
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86
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87 ]]></help>
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88 <citations>
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89 <citation type="doi">10.1093/bioinformatics/bts610</citation>
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90 </citations>
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91 </tool>