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