Mercurial > repos > bgruening > hicexplorer_hicplotsvl

comparison hicPlotSVL.xml @ 0:450605e43e25 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:50:36 -0500
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children 3a7752b8d2cb
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-1:000000000000 0:450605e43e25
1 <tool id="hicexplorer_hicplotsvl" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>plots the relation of short vs long range contacts</description>
3 <macros>
4 <token name="@BINARY@">hicPlotSVL</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10
11 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
12 #set identifier = @ESCAPE_IDENTIFIER_M@
13 ln -s '$m' '${counter}_$identifier' &&
14 #end for
15 #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
16
17 @BINARY@
18 --matrices $m
19 #if $distance:
20 --distance $distance
21 #end if
22
23 @CHROMOSOME_LIST@
24
25 #if $colorList:
26 #set $colorList_new = ' '.join([ '\'%s\'' % $color for $color in str($colorList).split(' ') ])
27 --colorList $colorList_new
28 #end if
29
30 #if $dpi:
31 --dpi $dpi
32 #end if
33 --plotFileName plot.$image_file_format
34 --outFileName p_values.txt
35 --outFileNameData ratios.txt
36 --threads @THREADS@
37
38 && mv plot.$image_file_format plot
39 ]]>
40 </command>
41 <inputs>
42 <expand macro='matrix_h5_cooler_multiple_macro'/>
43 <param argument="--distance" optional='true' type="integer" label="Short range distance"
44 help="Distance which should be considered as short range. Default 2MB." value='2000000'/>
45 <expand macro="chromosome_list" />
46 <param argument="--colorList" optional='true' type="text" label="Colorlist" help="Colorlist for the boxplots." />
47 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
48 <param name="image_file_format" type="select" label="Image output format">
49 <option value="png" selected="True">png</option>
50 <option value="svg">svg</option>
51 <option value="pdf">pdf</option>
52 </param>
53 </inputs>
54 <outputs>
55 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
56 <change_format>
57 <when input="image_file_format" value="svg" format="svg" />
58 <when input="image_file_format" value="pdf" format="pdf" />
59 </change_format>
60 </data>
61 <data name='output_p_values' from_work_dir='p_values.txt' format='txt' label='P values svl'/>
62 <data name='output_ratios' from_work_dir='ratios.txt' format='txt' label='Ratios svl'/>
63
64 </outputs>
65 <tests>
66 <test>
67 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
68 <param name="distance" value="2000000"/>
69 <param name="dpi" value="10"/>
70 <param name="color" value="y m c"/>
71 <repeat name="chromosome_list">
72 <param name="chromosomes" value="chr2L"/>
73 </repeat>
74 <repeat name="chromosome_list">
75 <param name="chromosomes" value="chr3L"/>
76 </repeat>
77 <repeat name="chromosome_list">
78 <param name="chromosomes" value="chr4"/>
79 </repeat>
80
81 <param name="image_file_format" value="png" />
82
83 <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size"/>
84 <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" compare="sim_size"/>
85 <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" compare="sim_size"/>
86
87 </test>
88 </tests>
89 <help><![CDATA[
90
91 Short vs long range contacts
92 ============================
93
94 Computes the ratio of short vs. long range contacts on the given matrices and makes, if two or more matrices are present a differential test between the matrices.
95
96 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
97
98 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
99
100 ]]></help>
101 <expand macro="citations" />
102 </tool>