Mercurial > repos > iuc > intervene
comparison intervene_upset.xml @ 0:f5fa293605ca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
author | iuc |
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date | Wed, 12 Sep 2018 13:22:43 -0400 |
parents | |
children | 33b8c5eedc04 |
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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> |