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comparison 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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-1:000000000000 0:f5fa293605ca
1 <tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@">
2 <description>and heatmap for genomic intervals</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">intervene</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 #import re
11 #set $labels = ",".join(["'%s'" % @ESCAPE_IDENTIFIER@ for file in $input])
12 #set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list'
13 intervene pairwise
14 --type $type
15 --input #echo " ".join(["'%s'" % file for file in $input])
16 --names $labels
17 --compute $compute
18 #if str($corrtype) != 'None'
19 --corr
20 --corrtype $corrtype
21 #end if
22 --htype $htype
23 $diagonal
24 --output results
25 --barcolor '$barcolor'
26 --fontsize '$fontsize'
27 --title '$title'
28 --figtype $figtype
29 --figsize $figsize_width $figsize_height
30 --dpi $dpi &&
31 mv results/Intervene_pairwise_*.${figtype} results/Intervene_pairwise.plot
32 ]]></command>
33 <inputs>
34 <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/>
35 <param argument="--compute" type="select" label="Use this metric for the heatmap">
36 <option value="count">count: calculates the number of overlaps</option>
37 <option value="frac" selected="true">frac: calculates the fraction of overlap</option>
38 <option value="jaccard">jaccard: calculate the Jaccard statistic</option>
39 <option value="reldist">reldist: calculate the distribution of relative distances</option>
40 <!-- fisher option needs additional genome assembly, probably triggers on demand download
41 <option value="fisher">fisher: calculate Fisher`s statistic</option>
42 -->
43 </param>
44 <param argument="--corrtype" type="select" label="Select the type of correlation">
45 <option value="None">Don't calculate correlation</option>
46 <option value="pearson">Pearson correlation</option>
47 <option value="kendall">Kendall correlation</option>
48 <option value="spearman">Spearman correlation</option>
49 </param>
50 <param argument="--htype" type="select" label="Heatmap plot type">
51 <option value="tribar">tribar</option>
52 <option value="dendrogram">dendrogram</option>
53 <option value="color">color</option>
54 <option value="pie">pie</option>
55 <option value="circle">circle</option>
56 <option value="square">square</option>
57 <option value="ellipse">ellipse</option>
58 <option value="number">number</option>
59 <option value="shade">shade</option>
60 </param>
61 <param argument="--diagonal" type="boolean" truevalue="--diagonal" falsevalue="" label="Show the diagonal values in the heatmap ?"/>
62 <!-- the argparse action is wrong for showsize, check this when upgrading tool in future -->
63 <param argument="--barcolor" type="color" label="Boxplot color" value="#53cfff">
64 <expand macro="color_sanitizer"/>
65 </param>
66 <param argument="--fontsize" type="integer" value="8" label="Label font size"/>
67 <param argument="--title" type="text" label="Heatmap main title" value="Pairwise intersection">
68 <expand macro="quote_sanitizer"/>
69 </param>
70 <expand macro="figure_params"/>
71 </inputs>
72 <outputs>
73 <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot">
74 <actions>
75 <action type="format">
76 <option type="from_param" name="figtype"/>
77 </action>
78 </actions>
79 </data>
80 </outputs>
81 <tests>
82 <test>
83 <param name="input" value="a.bed,b.bed,c.bed"/>
84 <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
85 </test>
86 </tests>
87 <help><![CDATA[
88 **What it does**
89
90 Plots the pairwise intersections of multiple interval files.
91
92 .. image:: $PATH_TO_IMAGES/pairwise.png
93
94 ]]></help>
95 <expand macro="citations"/>
96 </tool>