Mercurial > repos > mvdbeek > bam_readtagger

annotate plot_coverage.xml @ 80:c9361b7a025d draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a-dirty"
author mvdbeek
date Tue, 07 Apr 2020 15:25:30 -0400
parents c42dd2551c9c
children a446ab055307
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c42dd2551c9c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a"
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1 <tool id="plot_coverage" name="Plot coverage" version="0.5.25">
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2 <description>as area plot between BAM files</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.25">readtagger</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 #import re
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8 plot_coverage
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9 #for $r in $input_files
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10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
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11 --file '$r.input' '$identifier' $r.total_reads
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12 #end for
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13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind --style $style
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14 ]]></command>
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15 <inputs>
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16 <repeat name="input_files" title="Add input files to coverage plot" min="1">
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17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/>
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18 <param name="total_reads" type="integer" value="0" min="0" label="Total number of (mapped) reads. If given plot scale will be reads per million"/>
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19 </repeat>
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20 <param name="regions" type="text" label="Select regions to plot" optional="true" help="e.g X:1200000-1250000,X1250000-1300000. If left blank will plot all contigs/chromosomes.">
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21 <sanitizer>
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22 <valid initial="string.letters,string.digits">
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23 <add value="-" />
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24 <add value="," />
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25 <add value=":" />
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26 <add value="." />
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27 </valid>
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28 </sanitizer>
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29 </param>
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30 <param name="plot_kind" type="select" label="Select the plot type">
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31 <option value="area">Area plot</option>
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32 <option value="line">Line plot</option>
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33 </param>
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34 <param name="style" type="select" label="Select a plotting style">
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35 <option value="ggplot">ggplot</option>
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36 <option value="classic">classic</option>
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37 <option value="grayscale">greyscale</option>
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38 <option value="dark_background">dark_background</option>
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39 <option value="seaborn">seaborn</option>
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40 <option value="seaborn-bright">seaborn-bright</option>
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41 <option value="seaborn-colorblind">seaborn-colorblind</option>
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42 <option value="seaborn-dark">seaborn-dark</option>
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43 <option value="seaborn-dark-palette">seaborn-dark-palette</option>
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44 <option value="seaborn-darkgrid">seaborn-darkgrid</option>
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45 <option value="seaborn-deep">seaborn-deep</option>
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46 <option value="seaborn-muted">seaborn-muted</option>
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47 <option value="seaborn-notebook">seaborn-notebook</option>
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48 <option value="seaborn-paper">seaborn-paper</option>
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49 <option value="seaborn-pastel">seaborn-pastel</option>
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50 <option value="seaborn-poster">seaborn-poster</option>
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51 <option value="seaborn-talk">seaborn-talk</option>
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52 <option value="seaborn-ticks">seaborn-ticks</option>
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53 <option value="seaborn-white">seaborn-white</option>
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54 <option value="seaborn-whitegrid">seaborn-whitegrid</option>
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55 <option value="tableau-colorblind10">tableau-colorblind10</option>
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56 </param>
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57 </inputs>
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58 <outputs>
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59 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
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64 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
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65 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
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66 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
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67 <param name="regions" value="3R:13373525-13373615"/>
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68 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
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69 </test>
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70 <test>
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71 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
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72 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
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73 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
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74 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
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75 <param name="regions" value="3R:13373525-13373615"/>
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76 <param name="plot_kind" value="line"/>
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77 <output name="output" file="three_cluster_plot_line.pdf" ftype="pdf" compare="sim_size"/>
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78 </test>
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79 </tests>
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80 <help><![CDATA[
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81
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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82 This tool plots the coverage over a specified region (by default all chromosomes/contigs).
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
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240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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84 ]]></help>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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85 </tool>