Mercurial > repos > iuc > intervene

annotate intervene_pairwise.xml @ 2:33b8c5eedc04 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit bf6d77a84f796430a6b4530209d0f21e1d40d25a
author iuc
date Wed, 10 Aug 2022 08:23:43 +0000
parents f5fa293605ca
children 21beb30956c2
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33b8c5eedc04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit bf6d77a84f796430a6b4530209d0f21e1d40d25a
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1 <tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy1">
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2 <description>and heatmap for genomic intervals</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 pairwise
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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 --compute $compute
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21 #if str($corrtype) != 'None'
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22 --corr
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23 --corrtype $corrtype
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24 #end if
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25 --htype $htype
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26 $diagonal
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27 --output results
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28 --barcolor '$barcolor'
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29 --fontsize '$fontsize'
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30 --title '$title'
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31 --figtype $figtype
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32 --figsize $figsize_width $figsize_height
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33 --dpi $dpi &&
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34 mv results/Intervene_pairwise_*.${figtype} results/Intervene_pairwise.plot
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35 ]]></command>
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36 <inputs>
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37 <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/>
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38 <param argument="--compute" type="select" label="Use this metric for the heatmap">
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39 <option value="count">count: calculates the number of overlaps</option>
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40 <option value="frac" selected="true">frac: calculates the fraction of overlap</option>
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41 <option value="jaccard">jaccard: calculate the Jaccard statistic</option>
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42 <option value="reldist">reldist: calculate the distribution of relative distances</option>
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43 <!-- fisher option needs additional genome assembly, probably triggers on demand download
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44 <option value="fisher">fisher: calculate Fisher`s statistic</option>
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45 -->
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46 </param>
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47 <param argument="--corrtype" type="select" label="Select the type of correlation">
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48 <option value="None">Don't calculate correlation</option>
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49 <option value="pearson">Pearson correlation</option>
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50 <option value="kendall">Kendall correlation</option>
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51 <option value="spearman">Spearman correlation</option>
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52 </param>
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53 <param argument="--htype" type="select" label="Heatmap plot type">
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54 <option value="tribar">tribar</option>
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55 <option value="dendrogram">dendrogram</option>
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56 <option value="color">color</option>
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57 <option value="pie">pie</option>
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58 <option value="circle">circle</option>
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59 <option value="square">square</option>
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60 <option value="ellipse">ellipse</option>
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61 <option value="number">number</option>
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62 <option value="shade">shade</option>
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63 </param>
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64 <param argument="--diagonal" type="boolean" truevalue="--diagonal" falsevalue="" label="Show the diagonal values in the heatmap ?"/>
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65 <!-- the argparse action is wrong for showsize, check this when upgrading tool in future -->
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66 <param argument="--barcolor" type="color" label="Boxplot color" value="#53cfff">
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67 <expand macro="color_sanitizer"/>
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68 </param>
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69 <param argument="--fontsize" type="integer" value="8" label="Label font size"/>
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70 <param argument="--title" type="text" label="Heatmap main title" value="Pairwise intersection">
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71 <expand macro="quote_sanitizer"/>
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72 </param>
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73 <expand macro="figure_params"/>
2
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74 <param name="out_matrix" type="boolean" truevalue="true" falsevalue="false" label="Output the intervene matrix file?"/>
0
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75 </inputs>
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76 <outputs>
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77 <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot">
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78 <actions>
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79 <action type="format">
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80 <option type="from_param" name="figtype"/>
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81 </action>
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82 </actions>
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83 </data>
2
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84 <data name="matrix" format="txt" label="Matrix on ${on_string}" from_work_dir="results/Intervene_pairwise_frac_matrix.txt">
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85 <filter>out_matrix</filter>
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86 </data>
0
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87 </outputs>
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88 <tests>
2
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89 <test expect_num_outputs="2">
0
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90 <param name="input" value="a.bed,b.bed,c.bed"/>
2
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91 <param name="out_matrix" value="true"/>
0
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92 <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
2
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93 <output name="matrix" value="matrix.txt" />
0
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94 </test>
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95 </tests>
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96 <help><![CDATA[
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97 **What it does**
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98
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99 Plots the pairwise intersections of multiple interval files.
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100
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101 .. image:: $PATH_TO_IMAGES/pairwise.png
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102
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103 ]]></help>
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104 <expand macro="citations"/>
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105 </tool>