Mercurial > repos > iuc > hicexplorer_hicinterintratad

comparison hicInterIntraTAD.xml @ 0:68e6816a502a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:46:15 +0000
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1 <tool id="hicexplorer_hicinterintratad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>computes the ratio of inter TAD-scores vs. intra TADs</description>
3 <macros>
4 <token name="@BINARY@">hicInterIntraTAD</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
10
11 @BINARY@
12 --matrix 'matrix.$matrix_h5_cooler.ext'
13 --tadDomains '$tadDomains'
14
15 #if $fontSize:
16 --fontSize $fontSize
17 #end if
18
19 #if $dpi:
20 --dpi $dpi
21 #end if
22
23 --outFileName output_interintra.txt
24 --outFileNameRatioPlot plot.$image_file_format
25 --threads @THREADS@
26
27 && mv plot.$image_file_format plot
28
29 ]]> </command>
30 <inputs>
31 <expand macro="matrix_h5_cooler_macro" />
32 <param name="tadDomains" type="data" format="bed" label="Bed file with TAD domains coordinates" help="Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts, compute it for intra-domains." />
33
34 <expand macro="dpi" />
35 <param name="fontSize" type="integer" min="5" optional="True" label="Font size" help="Font size for the plot"/>
36
37 <param name="image_file_format" type="select" label="Image output format">
38 <option value="png" selected="True">png</option>
39 <option value="svg">svg</option>
40 <option value="pdf">pdf</option>
41 </param>
42
43 </inputs>
44 <outputs>
45 <data name='output_txt' from_work_dir='output_interintra.txt' format='txt' label='Intra Inter TAD ratios'/>
46
47 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
48 <change_format>
49 <when input="image_file_format" value="svg" format="svg" />
50 <when input="image_file_format" value="pdf" format="pdf" />
51 </change_format>
52 </data>
53 </outputs>
54 <tests>
55 <test>
56 <param name="matrix_h5_cooler" value="hicInterIntraTAD/matrix.cool" />
57 <param name="tadDomains" value="hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed" />
58
59 <output name="output_txt" file="hicInterIntraTAD/output.txt" ftype="txt" />
60
61 <output name="output_plot" file="hicInterIntraTAD/plot.png" ftype="png" />
62
63 </test>
64
65 </tests>
66 <help><![CDATA[
67
68 Calculate the ratio of inter-TAD contacts vs intra-TADs
69 =======================================================
70
71 Toplogical domains (TADs) are large mainly self-interacting domains. Chromatin interactions occur with higher frequency within a TAD as between TADs.
72 This tool supports to compute the ratio of contacts of a TAD (intra-TAD) with the contacts outside of it (inter-TAD).
73
74 For more information about HiCExplorer please consider our documentation on readthedocs.io_
75
76 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
77 ]]> </help>
78 <expand macro="citations" />
79 </tool>