Mercurial > repos > iuc > intervene

annotate intervene_pairwise.xml @ 0:f5fa293605ca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
author iuc
date Wed, 12 Sep 2018 13:22:43 -0400
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children 33b8c5eedc04
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f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
iuc
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1 <tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@">
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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2 <description>and heatmap for genomic intervals</description>
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">intervene</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #import re
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11 #set $labels = ",".join(["'%s'" % @ESCAPE_IDENTIFIER@ for file in $input])
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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12 #set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list'
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13 intervene pairwise
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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14 --type $type
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15 --input #echo " ".join(["'%s'" % file for file in $input])
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16 --names $labels
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17 --compute $compute
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18 #if str($corrtype) != 'None'
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19 --corr
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20 --corrtype $corrtype
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21 #end if
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22 --htype $htype
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23 $diagonal
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24 --output results
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25 --barcolor '$barcolor'
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26 --fontsize '$fontsize'
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27 --title '$title'
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28 --figtype $figtype
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29 --figsize $figsize_width $figsize_height
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30 --dpi $dpi &&
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31 mv results/Intervene_pairwise_*.${figtype} results/Intervene_pairwise.plot
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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32 ]]></command>
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33 <inputs>
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34 <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/>
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35 <param argument="--compute" type="select" label="Use this metric for the heatmap">
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36 <option value="count">count: calculates the number of overlaps</option>
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37 <option value="frac" selected="true">frac: calculates the fraction of overlap</option>
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38 <option value="jaccard">jaccard: calculate the Jaccard statistic</option>
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39 <option value="reldist">reldist: calculate the distribution of relative distances</option>
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40 <!-- fisher option needs additional genome assembly, probably triggers on demand download
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41 <option value="fisher">fisher: calculate Fisher`s statistic</option>
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42 -->
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43 </param>
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44 <param argument="--corrtype" type="select" label="Select the type of correlation">
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45 <option value="None">Don't calculate correlation</option>
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46 <option value="pearson">Pearson correlation</option>
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47 <option value="kendall">Kendall correlation</option>
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48 <option value="spearman">Spearman correlation</option>
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49 </param>
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50 <param argument="--htype" type="select" label="Heatmap plot type">
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51 <option value="tribar">tribar</option>
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52 <option value="dendrogram">dendrogram</option>
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53 <option value="color">color</option>
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54 <option value="pie">pie</option>
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55 <option value="circle">circle</option>
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56 <option value="square">square</option>
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57 <option value="ellipse">ellipse</option>
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58 <option value="number">number</option>
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59 <option value="shade">shade</option>
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60 </param>
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61 <param argument="--diagonal" type="boolean" truevalue="--diagonal" falsevalue="" label="Show the diagonal values in the heatmap ?"/>
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62 <!-- the argparse action is wrong for showsize, check this when upgrading tool in future -->
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63 <param argument="--barcolor" type="color" label="Boxplot color" value="#53cfff">
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64 <expand macro="color_sanitizer"/>
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65 </param>
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66 <param argument="--fontsize" type="integer" value="8" label="Label font size"/>
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67 <param argument="--title" type="text" label="Heatmap main title" value="Pairwise intersection">
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68 <expand macro="quote_sanitizer"/>
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69 </param>
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70 <expand macro="figure_params"/>
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71 </inputs>
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72 <outputs>
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73 <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot">
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74 <actions>
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75 <action type="format">
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76 <option type="from_param" name="figtype"/>
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77 </action>
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78 </actions>
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79 </data>
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="input" value="a.bed,b.bed,c.bed"/>
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84 <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
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85 </test>
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86 </tests>
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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87 <help><![CDATA[
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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88 **What it does**
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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89
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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90 Plots the pairwise intersections of multiple interval files.
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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91
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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92 .. image:: $PATH_TO_IMAGES/pairwise.png
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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93
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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94 ]]></help>
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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95 <expand macro="citations"/>
f5fa293605ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
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96 </tool>