Mercurial > repos > bgruening > hicexplorer_hicnormalize

comparison hicNormalize.xml @ 0:4f36f2d51d33 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 15:47:25 -0500
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children 483e507c8d42
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-1:000000000000 0:4f36f2d51d33
1 <tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>normalizes a matrix to norm range or smallest read count</description>
3 <macros>
4 <token name="@BINARY@">hicNormalize</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10
11 mkdir output &&
12 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
13 ln -s '$m' '${counter}_matrix.$m.ext' &&
14 #end for
15 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
16 #set $m_out = ' '.join([ "'output/%s_norm_%s'" % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
17
18 @BINARY@ --matrices $m
19 --normalize $normalize
20 --outFileName $m_out
21 ]]>
22 </command>
23 <inputs>
24 <expand macro='matrix_h5_cooler_multiple_macro'/>
25
26 <param name='normalize' type='select' label='Normalize matrices'>
27 <option value='norm_range'>0 to 1 range</option>
28 <option value='smallest'>Smallest read count</option>
29 </param>
30
31 </inputs>
32 <outputs>
33 <data name="normalize_matrix">
34 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true"/>
35 <!-- <change_format>
36 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/>
37 </change_format> -->
38 </data>
39
40 </outputs>
41 <tests>
42 <test>
43 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/>
44 <param name='normalize' value='norm_range'/>
45 <output name="normalize_matrix">
46 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
47 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
48 </discovered_dataset>
49 </output>
50 </test>
51
52 <test>
53 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>
54 <param name='normalize' value='smallest'/>
55
56 <output name="normalize_matrix">
57 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
58 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
59 </discovered_dataset>
60 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool">
61 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
62 </discovered_dataset>
63 </output>
64
65 </test>
66
67 <test>
68 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
69 <param name='normalize' value='smallest'/>
70
71 <output name="normalize_matrix">
72 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
73 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
74 </discovered_dataset>
75 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5">
76 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
77 </discovered_dataset>
78 </output>
79
80 </test>
81
82 </tests>
83 <help><![CDATA[
84 Normalization of matrices
85 =====================================
86
87 **hicNormalize** normalizes either each matrix to a 0 - 1 value range or to the smallest read coverage.
88
89 _________________
90
91 Output
92 ------
93
94 The normalized matrices.
95
96 _________________
97
98 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
99
100 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
101 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
102 ]]></help>
103 <expand macro="citations" />
104 </tool>