Mercurial > repos > iuc > intervene

annotate intervene_upset.xml @ 3:21beb30956c2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit f0241966e9185e5960947d12dcb490cce1fc6301
author iuc
date Fri, 21 Oct 2022 16:07:46 +0000
parents 33b8c5eedc04
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21beb30956c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit f0241966e9185e5960947d12dcb490cce1fc6301
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1 <tool id="intervene_upset" name="UpSet diagram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>of intersection of genomic regions or list sets</description>
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3 <xrefs>
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4 <xref type="bio.tools">intervene</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">intervene</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #import re
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14 #set $labels = ",".join(["'%s'" % @ESCAPE_IDENTIFIER@ for file in $input])
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15 #set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list'
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16 intervene upset
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17 --type $type
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18 --input #echo " ".join(["'%s'" % file for file in $input])
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19 --names $labels
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20 --output results
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21 --order $order
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22 --ninter $ninter
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23 $showzero
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24 $showsize
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25 --mbcolor '$mbcolor'
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26 --sbcolor '$sbcolor'
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27 --mblabel '$mblabel'
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28 --sxlabel '$sxlabel'
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29 --figtype $figtype
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30 --figsize $figsize_width $figsize_height
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31 --dpi $dpi &&
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32 mv results/Intervene_upset.${figtype} results/Intervene_upset.plot
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33 ]]></command>
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34 <inputs>
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35 <param argument="--input" type="data" format="txt" multiple="true" label="Select input files for which to produce intersections"/>
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36 <param argument="--order" type="select" label="Select the order of intersections of sets">
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37 <option value="freq">Frequency</option>
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38 <option value="degree">Degree</option>
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39 </param>
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40 <param argument="--ninter" type="integer" value="30" min="1" label="Number of top intersections to show in plot"/>
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41 <param argument="--showzero" type="boolean" truevalue="--showzero" falsevalue="" label="Show empty intersections in plot?"/>
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42 <!-- the argparse action is wrong for showsize, check this when upgrading tool in future -->
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43 <param argument="--showsize" type="boolean" truevalue="" falsevalue="--showsize" checked="true" label="Show intersection sizes above bars ?"/>
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44 <param argument="--mbcolor" type="color" label="Color of the main bar plot" value="#ea5d4e">
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45 <expand macro="color_sanitizer"/>
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46 </param>
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47 <param argument="--sbcolor" type="color" label="Color of the set size bar plot" value="#317eab">
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48 <expand macro="color_sanitizer"/>
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49 </param>
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50 <param argument="--mblabel" type="text" label="The y-axis label of the intersection size bars" value="No. of Intersections">
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51 <expand macro="quote_sanitizer"/>
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52 </param>
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53 <param argument="--sxlabel" type="text" label="The x-axis label of the set size bars" value="Set size">
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54 <expand macro="quote_sanitizer"/>
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55 </param>
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56 <expand macro="figure_params"/>
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57 </inputs>
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58 <outputs>
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59 <data name="plot" format="pdf" label="UpSet plot on ${on_string}" from_work_dir="results/Intervene_upset.plot">
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60 <actions>
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61 <action type="format">
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62 <option type="from_param" name="figtype"/>
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63 </action>
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64 </actions>
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65 </data>
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="input" value="a.txt,b.txt,c.txt"/>
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70 <output name="plot" value="upset.pdf" compare="sim_size"/>
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71 </test>
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72 <test>
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73 <param name="input" value="a.bed,b.bed,c.bed"/>
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74 <output name="plot" value="bed_upset.pdf" compare="sim_size"/>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 **What it does**
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79
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80 This tool produces an upset plot for the intersection of sets from different datasets.
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81 These can be regular lists or BED/GFF/interval files which will be processed using bedtools intersect.
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82
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83 .. image:: $PATH_TO_IMAGES/upset.png
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84
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85 ]]></help>
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86 <expand macro="citations"/>
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
iuc
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87 </tool>