Mercurial > repos > bgruening > hicexplorer_hicfindtads

comparison hicFindTADs.xml @ 5:db2cc9e1ff76 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:39:05 -0500
parents 8b60271e7e54
children b05f292d220c
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4:8b60271e7e54 5:db2cc9e1ff76
4 <token name="@BINARY@">hicFindTADs</token> 4 <token name="@BINARY@">hicFindTADs</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9
10 hicFindTADs 9 hicFindTADs
11 --matrix '$matrix' 10 --matrix '$matrix_h5_cooler'
12 11
13 --delta $delta 12 --delta $delta
14 13
15 #if $minBoundaryDistance: 14 #if $minBoundaryDistance:
16 --minBoundaryDistance $minBoundaryDistance 15 --minBoundaryDistance $minBoundaryDistance
30 29
31 --numberOfProcessors @THREADS@ 30 --numberOfProcessors @THREADS@
32 --outPrefix galaxy_tad_prefix 31 --outPrefix galaxy_tad_prefix
33 ]]></command> 32 ]]></command>
34 <inputs> 33 <inputs>
35 <param argument="--matrix" type="data" format="h5" label="Corrected Hi-C matrix to use for the computations"/> 34 <expand macro='matrix_h5_cooler_macro' />
35
36 <param argument="--minDepth" type="integer" value="40000" 36 <param argument="--minDepth" type="integer" value="40000"
37 label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin." 37 label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
38 help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/> 38 help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>
39 <param argument="--maxDepth" type="integer" value="100000" 39 <param argument="--maxDepth" type="integer" value="100000"
40 label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin." 40 label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
91 <data name="matrix_output" from_work_dir="galaxy_tad_prefix_zscore_matrix.h5" 91 <data name="matrix_output" from_work_dir="galaxy_tad_prefix_zscore_matrix.h5"
92 format="h5" label="${tool.name} on ${on_string}: Z-score matrix in h5" /> 92 format="h5" label="${tool.name} on ${on_string}: Z-score matrix in h5" />
93 </outputs> 93 </outputs>
94 <tests> 94 <tests>
95 <test> 95 <test>
96 <param name="matrix" value="small_test_matrix.h5" ftype="h5" /> 96 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
97
97 <param name="minDepth" value="60000"/> 98 <param name="minDepth" value="60000"/>
98 <param name="maxDepth" value="180000"/> 99 <param name="maxDepth" value="180000"/>
99 <param name="step" value="20000"/> 100 <param name="step" value="20000"/>
100 <param name="minBoundaryDistance" value="20000" /> 101 <param name="minBoundaryDistance" value="20000" />
101 <conditional name="multiple_comparison_conditional"> 102 <conditional name="multiple_comparison_conditional">
123 “The absolute value of z represents the distance between the raw score and the population mean in 124 “The absolute value of z represents the distance between the raw score and the population mean in
124 units of the standard deviation. z is negative when the raw score is below the mean, positive when above.” 125 units of the standard deviation. z is negative when the raw score is below the mean, positive when above.”
125 [Source_]. 126 [Source_].
126 127
127 .. image:: $PATH_TO_IMAGES/z-score.svg 128 .. image:: $PATH_TO_IMAGES/z-score.svg
128 :width: 150 129 :width: 100
129 130
130 `Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_ 131 `Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_
131 132
132 In our case the distribution describes the counts per bin of a genomic distance. In a second step the local minima of the TAD-separation score is evaluated with respect to the surrounding bins to assign a p-value. Two multiple testing corrections can be applied to filter the results: `Bonferroni <https://en.wikipedia.org/wiki/Bonferroni_correction>`_ or the `false discovery rate <https://en.wikipedia.org/wiki/False_discovery_rate>`_. 133 In our case the distribution describes the counts per bin of a genomic distance. In a second step the local minima of the TAD-separation score is evaluated with respect to the surrounding bins to assign a p-value. Two multiple testing corrections can be applied to filter the results: `Bonferroni <https://en.wikipedia.org/wiki/Bonferroni_correction>`_ or the `false discovery rate <https://en.wikipedia.org/wiki/False_discovery_rate>`_.
133 134