Mercurial > repos > bgruening > hicexplorer_hicplotsvl

comparison hicPlotSVL.xml @ 2:3a7752b8d2cb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 17:00:23 -0400
parents 450605e43e25
children b75f87deaa15
comparison
equal deleted inserted replaced
1:ec91f79c59bb 2:3a7752b8d2cb
11 #for $counter, $m in enumerate($matrix_h5_cooler_multiple): 11 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
12 #set identifier = @ESCAPE_IDENTIFIER_M@ 12 #set identifier = @ESCAPE_IDENTIFIER_M@
13 ln -s '$m' '${counter}_$identifier' && 13 ln -s '$m' '${counter}_$identifier' &&
14 #end for 14 #end for
15 #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) 15 #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
16 16
17 @BINARY@ 17 @BINARY@
18 --matrices $m 18 --matrices $m
19 #if $distance: 19 #if $distance:
20 --distance $distance 20 --distance $distance
21 #end if 21 #end if
27 --colorList $colorList_new 27 --colorList $colorList_new
28 #end if 28 #end if
29 29
30 #if $dpi: 30 #if $dpi:
31 --dpi $dpi 31 --dpi $dpi
32 #end if 32 #end if
33 --plotFileName plot.$image_file_format 33 --plotFileName plot.$image_file_format
34 --outFileName p_values.txt 34 --outFileName p_values.txt
35 --outFileNameData ratios.txt 35 --outFileNameData ratios.txt
36 --threads @THREADS@ 36 --threads @THREADS@
37 37
38 && mv plot.$image_file_format plot 38 && mv plot.$image_file_format plot
39 ]]> 39 ]]>
40 </command> 40 </command>
49 <option value="png" selected="True">png</option> 49 <option value="png" selected="True">png</option>
50 <option value="svg">svg</option> 50 <option value="svg">svg</option>
51 <option value="pdf">pdf</option> 51 <option value="pdf">pdf</option>
52 </param> 52 </param>
53 </inputs> 53 </inputs>
54 <outputs> 54 <outputs>
55 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'> 55 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
56 <change_format> 56 <change_format>
57 <when input="image_file_format" value="svg" format="svg" /> 57 <when input="image_file_format" value="svg" format="svg" />
58 <when input="image_file_format" value="pdf" format="pdf" /> 58 <when input="image_file_format" value="pdf" format="pdf" />
59 </change_format> 59 </change_format>
81 <param name="image_file_format" value="png" /> 81 <param name="image_file_format" value="png" />
82 82
83 <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size"/> 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"/> 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"/> 85 <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" compare="sim_size"/>
86 86
87 </test> 87 </test>
88 </tests> 88 </tests>
89 <help><![CDATA[ 89 <help><![CDATA[
90 90
91 Short vs long range contacts 91 Short vs long range contacts
92 ============================ 92 ============================
93 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. 94 hicPlotSVL computes the ratio between short range and long range contacts per chromosome independently. Per sample one box plot is created and,
95 if more than one sample is given, the computed ratios are assumed to be one distribution and a Wilcoxon rank-sum test under H0 'distributions are equal'
96 is computed. All used data is written to a third raw data file.
97
98 The distance to distinct short and long range contacts can be set via the –distance parameter; for short range the sum for all contacts smaller or equal this distance are computed, for long range contacts all contacts greater this distance.
99
100
101
102 Usage
103 -----
104
105
106 .. code-block:: text
107
108 $ hicPlotSVL -m hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool --distance 2000000 --threads 4 --plotFileName plot.png --outFileName pvalues.txt --outFileNameData rawData.txt
109
110
111 This results in three files:
112
113 The raw data containing the sums for short range, long range and ratio per sample and chromosome.
114
115
116 .. code-block:: text
117
118 # Created with HiCExplorer's hicPlotSVL 3.3
119 # Short range vs long range contacts per chromosome: raw data
120 # Short range contacts: <= 2000000
121 # hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool
122 # Chromosome Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000
123 1 3.0399769346724543 33476834 11012200 2.79740105237572 44262902 15822866 3.0399769346724543 33476834 11012200
124 2 2.7532203542810625 31723954 11522490 2.5007877714355438 47468438 18981394 2.7532203542810625 31723954 11522490
125 3 2.922650759458664 26251027 8981924 2.6235211241878442 39640848 15109788 2.922650759458664 26251027 8981924
126 4 2.7235598858451637 22474680 8251950 2.5572455199457864 37486882 14659086 2.7235598858451637 22474680 8251950
127 5 2.9585962905193712 22716268 7678056 2.752922527526723 35445722 12875670 2.9585962905193712 22716268 7678056
128 6 3.168274165465025 22872690 7219290 2.8602111006131703 33990211 11883812 3.168274165465025 22872690 7219290
129 7 3.1093346580597516 19603416 6304698 2.8021236966788887 29712823 10603680 3.1093346580597516 19603416 6304698
130 8 3.135391026076832 18355087 5854162 2.7964394470859024 28660624 10248970 3.135391026076832 18355087 5854162
131 9 4.1147978383348125 15395763 3741560 3.819940066283481 21994046 5757694 4.1147978383348125 15395763 3741560
132 10 3.448063050802953 17964043 5209894 3.1116673856502253 26270171 8442474 3.448063050802953 17964043 5209894
133 11 3.5924666993070407 18651850 5191934 3.1364875011923035 26240350 8366158 3.5924666993070407 18651850 5191934
134 12 3.6817551043464416 18640866 5063038 3.306662109403207 26101554 7893626 3.6817551043464416 18640866 5063038
135 13 3.476204237522881 11018462 3169682 3.0976674036654805 18922281 6108558 3.476204237522881 11018462 3169682
136 14 3.70550850832778 11164875 3013048 3.6226817463785164 17245704 4760480 3.70550850832778 11164875 3013048
137 15 4.607631079612186 11165313 2423222 4.567998349104569 15273742 3343640 4.607631079612186 11165313 2423222
138 16 4.397874357146307 10745775 2443402 3.890983210350018 14666462 3769346 4.397874357146307 10745775 2443402
139 17 5.809374740402161 12168235 2094586 5.3360710927739285 14154110 2652534 5.809374740402161 12168235 2094586
140 18 3.7647349280938895 9339833 2480874 3.485487446356812 15019063 4309028 3.7647349280938895 9339833 2480874
141 19 6.492239632778196 8466283 1304062 5.774337450385819 9368978 1622520 6.492239632778196 8466283 1304062
142 20 5.542933774973686 8962935 1617002 4.977679877778358 12009479 2412666 5.542933774973686 8962935 1617002
143 21 6.665622315255486 3910374 586648 6.1843701763589225 6554715 1059884 6.665622315255486 3910374 586648
144 22 8.063663557923096 4992327 619114 7.433759425439728 5932928 798106 8.063663557923096 4992327 619114
145 X 2.208752982178897 14424173 6530460 2.3130534357407995 27628734 11944702 2.208752982178897 14424173 6530460
146 Y 4.165021803993573 36294 8714 3.8063291139240505 45105 11850 4.165021803993573 36294 8714
147 MT
148
149
150
151 The p-values between the samples:
152
153 .. code-block:: text
154
155 # Created with HiCExplorer's hicPlotSVL 3.3
156 # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
157 # Short range contacts: <= 2000000
158 hmec_10kb.cool nhek_10kb.cool 0.28362036331636575
159 hmec_10kb.cool hmec_10kb.cool 1.0
160 nhek_10kb.cool hmec_10kb.cool 0.28362036331636575
161
162
163
164 The box plot:
165
166 .. image:: $PATH_TO_IMAGES/plot_svl.png
167 :width: 50%
95 168
96 For more information about HiCExplorer please consider our documentation on readthedocs.io_. 169 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
97 170
98 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 171 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
99 172