Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 19:e4cb7809df61 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:41:08 +0000
parents c543c41377dd
children f5a37c3906cc
comparison
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18:5443b2b1165f 19:e4cb7809df61
1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>run a Hi-C matrix correction algorithm</description> 2 <description>run a Hi-C matrix correction algorithm</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicCorrectMatrix</token> 4 <token name="@BINARY@">hicCorrectMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
66 <option value="diagnostic_plot">Diagnostic plot</option> 66 <option value="diagnostic_plot">Diagnostic plot</option>
67 <option value="correct">Correct matrix</option> 67 <option value="correct">Correct matrix</option>
68 </param> 68 </param>
69 <when value="diagnostic_plot"> 69 <when value="diagnostic_plot">
70 <expand macro="xMax" /> 70 <expand macro="xMax" />
71 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" 71 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
72 label="Compute statistics for each chromosome separately" />
73 </when> 72 </when>
74 <when value="correct"> 73 <when value="correct">
75 <conditional name='correctionMethod'> 74 <conditional name='correctionMethod'>
76 <param name='correctionMethod_selector' type='select' label='Correction method'> 75 <param name='correctionMethod_selector' type='select' label='Correction method'>
77 <option value='ice'>Iterative_correction (Imakaev)</option> 76 <option value='ice'>Iterative_correction (Imakaev)</option>
78 <option value='kr'>Knights-Ruiz</option> 77 <option value='kr'>Knights-Ruiz</option>
79 </param> 78 </param>
80 79
81 <when value='ice'> 80 <when value='ice'>
82 <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" 81 <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
83 label="Number of iterations" /> 82
84 83 <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
85 <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" 84 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." />
86 label="Inflation cutoff" value="" 85
87 help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction. 86 <param argument="--transCutoff" name="transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." />
88 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/> 87
89 88 <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads.
90 <param argument="--transCutoff" name="transCutoff" type="float" optional="true" 89 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered." />
91 label="Trans region cutoff" value="" 90
92 help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/> 91 <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" />
93 92
94 <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" 93 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
95 label="Sequenced count cutoff"
96 help="Each bin receives a value indicating the fraction that is covered by reads.
97 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/>
98
99 <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false"
100 label="Skip diagonal counts"/>
101
102 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
103 label="Normalize each chromosome separately" />
104 <expand macro="filterThreshold" /> 94 <expand macro="filterThreshold" />
105 </when> 95 </when>
106 <when value='kr'> 96 <when value='kr'>
107 </when> 97 </when>
108 </conditional> 98 </conditional>
109 </when> 99 </when>
110 </conditional> 100 </conditional>
111 101
112 <repeat name="chromosomes" min="0" 102 <repeat name="chromosomes" min="0" title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
113 title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
114 The order of the given chromosomes will be kept for the resulting corrected matrix"> 103 The order of the given chromosomes will be kept for the resulting corrected matrix">
115 <param name="chromosome" type="text" value="" label='chromosome (one per field)'> 104 <param name="chromosome" type="text" value="" label='chromosome (one per field)'>
116 <validator type="empty_field" /> 105 <validator type="empty_field" />
117 </param> 106 </param>
118 </repeat> 107 </repeat>
119 108
120 </inputs> 109 </inputs>
121 <outputs> 110 <outputs>
122 <data name="outFileName" from_work_dir="matrix" format="cool"> 111 <data name="outFileName" from_work_dir="matrix" format="cool">
123 <change_format> 112 <change_format>
124 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/> 113 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
125 </change_format> 114 </change_format>
126 <filter>mode['mode_selector'] == "correct"</filter> 115 <filter>mode['mode_selector'] == "correct"</filter>
127
128 </data> 116 </data>
129
130
131 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png"> 117 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
132 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> 118 <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
133 </data> 119 </data>
134 </outputs> 120 </outputs>
135 <tests> 121 <tests>
136 <test> 122 <test>
137 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 123 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
138 124 <param name="mode_selector" value="correct" />
139 <param name="mode_selector" value="correct"/> 125 <param name='correctionMethod_selector' value='ice' />
140 <param name='correctionMethod_selector' value='ice'/> 126 <repeat name="chromosomes">
141 <repeat name="chromosomes"> 127 <param name="chromosome" value="chrUextra" />
142 <param name="chromosome" value="chrUextra"/> 128 </repeat>
143 </repeat> 129 <repeat name="chromosomes">
144 <repeat name="chromosomes"> 130 <param name="chromosome" value="chr3LHet" />
145 <param name="chromosome" value="chr3LHet"/>
146 </repeat> 131 </repeat>
147 <param name='filterThreshold_low' value='-2.0' /> 132 <param name='filterThreshold_low' value='-2.0' />
148 <param name='filterThreshold_large' value='4' /> 133 <param name='filterThreshold_large' value='4' />
149 <output name="outFileName" ftype="h5"> 134 <output name="outFileName" ftype="h5">
150 <assert_contents> 135 <assert_contents>
151 <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins'/> 136 <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' />
152 </assert_contents> 137 </assert_contents>
153 </output> 138 </output>
154 </test> 139 </test>
155 <test> 140 <test>
156 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 141 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
157 142 <param name="mode_selector" value="correct" />
158 <param name="mode_selector" value="correct"/> 143 <param name='correctionMethod_selector' value='kr' />
159 <param name='correctionMethod_selector' value='kr'/>
160
161 <output name="outFileName" ftype="h5"> 144 <output name="outFileName" ftype="h5">
162 <assert_contents> 145 <assert_contents>
163 <has_h5_keys keys='correction_factors,intervals,matrix'/> 146 <has_h5_keys keys='correction_factors,intervals,matrix' />
164 </assert_contents> 147 </assert_contents>
165 </output> 148 </output>
166 </test> 149 </test>
167 <test> 150 <test>
168 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> 151 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
169 152 <param name="mode_selector" value="correct" />
170 <param name="mode_selector" value="correct"/> 153 <param name='correctionMethod_selector' value='kr' />
171 <param name='correctionMethod_selector' value='kr'/>
172
173 <output name="outFileName" ftype="cool"> 154 <output name="outFileName" ftype="cool">
174 <assert_contents> 155 <assert_contents>
175 <has_h5_keys keys='bins,chroms,indexes,pixels'/> 156 <has_h5_keys keys='bins,chroms,indexes,pixels' />
176 </assert_contents> 157 </assert_contents>
177 </output> 158 </output>
178 </test> 159 </test>
179 <test> 160 <test>
180 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 161 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
181 162
182 <param name="mode_selector" value="correct"/> 163 <param name="mode_selector" value="correct" />
183 <param name='correctionMethod_selector' value='ice'/> 164 <param name='correctionMethod_selector' value='ice' />
184 <repeat name="chromosomes"> 165 <repeat name="chromosomes">
185 <param name="chromosome" value="chrUextra"/> 166 <param name="chromosome" value="chrUextra" />
186 </repeat> 167 </repeat>
187 <repeat name="chromosomes"> 168 <repeat name="chromosomes">
188 <param name="chromosome" value="chr3LHet"/> 169 <param name="chromosome" value="chr3LHet" />
189 </repeat> 170 </repeat>
190 <param name='filterThreshold_low' value='-2.0' /> 171 <param name='filterThreshold_low' value='-2.0' />
191 <param name='filterThreshold_large' value='4' /> 172 <param name='filterThreshold_large' value='4' />
192 <output name="outFileName" ftype="h5"> 173 <output name="outFileName" ftype="h5">
193 <assert_contents> 174 <assert_contents>
194 <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins'/> 175 <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' />
195 </assert_contents> 176 </assert_contents>
196 </output> 177 </output>
197 </test> 178 </test>
198 <test> 179 <test>
199 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 180 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
200 <param name="mode_selector" value="diagnostic_plot"/> 181 <param name="mode_selector" value="diagnostic_plot" />
201 <repeat name="chromosomes"> 182 <repeat name="chromosomes">
202 <param name="chromosome" value="chrUextra"/> 183 <param name="chromosome" value="chrUextra" />
203 </repeat> 184 </repeat>
204 <repeat name="chromosomes"> 185 <repeat name="chromosomes">
205 <param name="chromosome" value="chr3LHet"/> 186 <param name="chromosome" value="chr3LHet" />
206 </repeat> 187 </repeat>
207 <output name="diagnostic_plot" file="hicCorrectMatrix/diagnostic_plot.png" ftype="png" compare="sim_size"/> 188 <output name="diagnostic_plot" file="hicCorrectMatrix/diagnostic_plot.png" ftype="png" compare="sim_size" />
208 </test> 189 </test>
209 </tests> 190 </tests>
210 <help><![CDATA[ 191 <help><![CDATA[
211 192
212 Hi-C contact matrix correction 193 Hi-C contact matrix correction
273 254
274 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 255 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
275 256
276 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 257 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
277 .. _`Imakaev et al. (2012)`: https://doi.org/10.1038/nmeth.2148 258 .. _`Imakaev et al. (2012)`: https://doi.org/10.1038/nmeth.2148
278 ]]></help> 259 ]]> </help>
279 <expand macro="citations" /> 260 <expand macro="citations" />
280 </tool> 261 </tool>