Mercurial > repos > bgruening > hicexplorer_hicnormalize

comparison hicNormalize.xml @ 1:483e507c8d42 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
author bgruening
date Wed, 05 Feb 2020 20:01:26 -0500
parents 4f36f2d51d33
children 05257e5d5016
comparison
equal deleted inserted replaced
0:4f36f2d51d33 1:483e507c8d42
14 #end for 14 #end for
15 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) 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) ]) 16 #set $m_out = ' '.join([ "'output/%s_norm_%s'" % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
17 17
18 @BINARY@ --matrices $m 18 @BINARY@ --matrices $m
19 --normalize $normalize 19 #if $normalize_conditional.normalize == 'multiplicative':
20 --multiplicativeValue $normalize_conditional.multiplicativeValue
21 #end if
22 --normalize $normalize_conditional.normalize
23 #if $zero_threshold_value:
24 --setToZeroThreshold $zero_threshold_value
25 #end if
26
20 --outFileName $m_out 27 --outFileName $m_out
21 ]]> 28 ]]>
22 </command> 29 </command>
23 <inputs> 30 <inputs>
24 <expand macro='matrix_h5_cooler_multiple_macro'/> 31 <expand macro='matrix_h5_cooler_multiple_macro'/>
25 32 <conditional name="normalize_conditional">
26 <param name='normalize' type='select' label='Normalize matrices'> 33 <param name='normalize' type='select' label='Normalize matrices'>
27 <option value='norm_range'>0 to 1 range</option> 34 <option value='norm_range'>0 to 1 range</option>
28 <option value='smallest'>Smallest read count</option> 35 <option value='smallest'>Smallest read count</option>
29 </param> 36 <option value='multiplicative'>Multiply by value</option>
30 37 </param>
38 <when value='norm_range'/>
39 <when value='smallest'/>
40 <when value='multiplicative'>
41 <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value"/>
42 </when>
43 </conditional>
44 <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero"/>
31 </inputs> 45 </inputs>
32 <outputs> 46 <outputs>
33 <data name="normalize_matrix"> 47 <data format='cool' name="normalize_matrix">
34 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true"/> 48 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true"/>
35 <!-- <change_format> 49 <change_format>
36 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/> 50 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/>
37 </change_format> --> 51 </change_format>
38 </data> 52 </data>
39
40 </outputs> 53 </outputs>
41 <tests> 54 <tests>
42 <test> 55 <test>
43 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/> 56 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/>
44 <param name='normalize' value='norm_range'/> 57 <param name='normalize' value='norm_range'/>
46 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> 59 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
47 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> 60 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
48 </discovered_dataset> 61 </discovered_dataset>
49 </output> 62 </output>
50 </test> 63 </test>
51
52 <test> 64 <test>
53 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/> 65 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>
54 <param name='normalize' value='smallest'/> 66 <param name='normalize' value='smallest'/>
55
56 <output name="normalize_matrix"> 67 <output name="normalize_matrix">
57 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> 68 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
58 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> 69 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
59 </discovered_dataset> 70 </discovered_dataset>
60 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool"> 71 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool">
61 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents> 72 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
62 </discovered_dataset> 73 </discovered_dataset>
63 </output> 74 </output>
64
65 </test> 75 </test>
66
67 <test> 76 <test>
68 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/> 77 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
69 <param name='normalize' value='smallest'/> 78 <param name='normalize' value='smallest'/>
70
71 <output name="normalize_matrix"> 79 <output name="normalize_matrix">
72 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> 80 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
73 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents> 81 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
74 </discovered_dataset> 82 </discovered_dataset>
75 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5"> 83 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5">
76 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents> 84 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
77 </discovered_dataset> 85 </discovered_dataset>
78 </output> 86 </output>
79
80 </test> 87 </test>
81
82 </tests> 88 </tests>
83 <help><![CDATA[ 89 <help><![CDATA[
84 Normalization of matrices 90 Normalization of matrices
85 ===================================== 91 =========================
86 92
87 **hicNormalize** normalizes either each matrix to a 0 - 1 value range or to the smallest read coverage. 93 **hicNormalize** normalizes either each matrix to a 0 - 1 value range, to the smallest read coverage or with a user given factor.
88 94
89 _________________ 95 _________________
90 96
91 Output 97 Output
92 ------ 98 ------