Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 15:c543c41377dd 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 06:53:35 -0400
parents 1e622e371512
children e4cb7809df61
comparison
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14:1e622e371512 15:c543c41377dd
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 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && 9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
10 10
11 @BINARY@ 11 @BINARY@
12 $mode.mode_selector 12 $mode.mode_selector
13 --matrix 'matrix.$matrix_h5_cooler.ext' 13 --matrix 'matrix.$matrix_h5_cooler.ext'
14 14
15 ## special: --chromosomes is optional, but if given needs at least one argument 15 ## special: --chromosomes is optional, but if given needs at least one argument
20 20
21 #if $mode.mode_selector == 'correct': 21 #if $mode.mode_selector == 'correct':
22 #if $mode.correctionMethod.correctionMethod_selector == 'ice': 22 #if $mode.correctionMethod.correctionMethod_selector == 'ice':
23 --correctionMethod ICE 23 --correctionMethod ICE
24 --iterNum $mode.correctionMethod.iterNum 24 --iterNum $mode.correctionMethod.iterNum
25 25
26 26
27 #if $mode.correctionMethod.filterThreshold_low and $mode.correctionMethod.filterThreshold_large: 27 #if $mode.correctionMethod.filterThreshold_low and $mode.correctionMethod.filterThreshold_large:
28 --filterThreshold $mode.correctionMethod.filterThreshold_low $mode.correctionMethod.filterThreshold_large 28 --filterThreshold $mode.correctionMethod.filterThreshold_low $mode.correctionMethod.filterThreshold_large
29 #end if 29 #end if
30 30
155 <test> 155 <test>
156 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 156 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
157 157
158 <param name="mode_selector" value="correct"/> 158 <param name="mode_selector" value="correct"/>
159 <param name='correctionMethod_selector' value='kr'/> 159 <param name='correctionMethod_selector' value='kr'/>
160 160
161 <output name="outFileName" ftype="h5"> 161 <output name="outFileName" ftype="h5">
162 <assert_contents> 162 <assert_contents>
163 <has_h5_keys keys='correction_factors,intervals,matrix'/> 163 <has_h5_keys keys='correction_factors,intervals,matrix'/>
164 </assert_contents> 164 </assert_contents>
165 </output> 165 </output>
167 <test> 167 <test>
168 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> 168 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
169 169
170 <param name="mode_selector" value="correct"/> 170 <param name="mode_selector" value="correct"/>
171 <param name='correctionMethod_selector' value='kr'/> 171 <param name='correctionMethod_selector' value='kr'/>
172 172
173 <output name="outFileName" ftype="cool"> 173 <output name="outFileName" ftype="cool">
174 <assert_contents> 174 <assert_contents>
175 <has_h5_keys keys='bins,chroms,indexes,pixels'/> 175 <has_h5_keys keys='bins,chroms,indexes,pixels'/>
176 </assert_contents> 176 </assert_contents>
177 </output> 177 </output>
252 the histogram follows a bimodal distribution where the first peak is for bins with zero reads which usually occur 252 the histogram follows a bimodal distribution where the first peak is for bins with zero reads which usually occur
253 at repetitive regions. Other low scoring bins tend to be close to repetitive regions. 253 at repetitive regions. Other low scoring bins tend to be close to repetitive regions.
254 Also, low scoring bins can be caused by absence of a restriction site in the bin or because the restriction 254 Also, low scoring bins can be caused by absence of a restriction site in the bin or because the restriction
255 site is present but the restriction enzyme did not cut. The valley between the two peaks in the 255 site is present but the restriction enzyme did not cut. The valley between the two peaks in the
256 histogram is set by default as cutoff threshold. 256 histogram is set by default as cutoff threshold.
257 However, it is important to revise this as in some cases the selected value could not be correct. 257 However, it is important to revise this as in some cases the selected value could not be correct.
258 258
259 259
260 .. image:: $PATH_TO_IMAGES/diagnostic_plot.png 260 .. image:: $PATH_TO_IMAGES/diagnostic_plot.png
261 :width: 50% 261 :width: 50%
262 262