Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 21:ea19190ce5e0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:20:07 +0000
parents f5a37c3906cc
children 62b720dceb56
comparison
equal deleted inserted replaced
20:f5a37c3906cc 21:ea19190ce5e0
58 && mv matrix.$matrix_h5_cooler.ext '$outFileName' 58 && mv matrix.$matrix_h5_cooler.ext '$outFileName'
59 #end if 59 #end if
60 ]]> 60 ]]>
61 </command> 61 </command>
62 <inputs> 62 <inputs>
63 <expand macro='matrix_h5_cooler_macro' /> 63 <expand macro="matrix_h5_cooler_macro" />
64 <conditional name="mode"> 64 <conditional name="mode">
65 <param name="mode_selector" type="select" label="Mode"> 65 <param name="mode_selector" type="select" label="Mode">
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" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" /> 71 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
72 </when> 72 </when>
73 <when value="correct"> 73 <when value="correct">
74 <conditional name='correctionMethod'> 74 <conditional name="correctionMethod">
75 <param name='correctionMethod_selector' type='select' label='Correction method'> 75 <param name="correctionMethod_selector" type="select" label="Correction method">
76 <option value='ice'>Iterative_correction (Imakaev)</option> 76 <option value="ice">Iterative_correction (Imakaev)</option>
77 <option value='kr'>Knights-Ruiz</option> 77 <option value="kr">Knights-Ruiz</option>
78 </param> 78 </param>
79 79
80 <when value='ice'> 80 <when value="ice">
81 <param argument="--iterNum" type="integer" optional="true" value="500" label="Number of iterations" /> 81 <param argument="--iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
82 82
83 <param argument="--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. 83 <param argument="--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.
84 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." /> 84 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." />
85 85
91 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" /> 91 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" />
92 92
93 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" /> 93 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
94 <expand macro="filterThreshold" /> 94 <expand macro="filterThreshold" />
95 </when> 95 </when>
96 <when value='kr'> 96 <when value="kr">
97 </when> 97 </when>
98 </conditional> 98 </conditional>
99 </when> 99 </when>
100 </conditional> 100 </conditional>
101 101
102 <repeat name="chromosomes" min="0" title="Include chromosomes" help="List of chromosomes to be included in the iterative correction. 102 <repeat name="chromosomes" min="0" title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
103 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">
104 <param name="chromosome" type="text" value="" label='chromosome (one per field)'> 104 <param name="chromosome" type="text" value="" label="chromosome (one per field)">
105 <validator type="empty_field" /> 105 <validator type="empty_field" />
106 </param> 106 </param>
107 </repeat> 107 </repeat>
108 108
109 </inputs> 109 </inputs>
117 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png" label="${tool.name} on ${on_string}: Diagnostic plot"> 117 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png" label="${tool.name} on ${on_string}: Diagnostic plot">
118 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> 118 <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
119 </data> 119 </data>
120 </outputs> 120 </outputs>
121 <tests> 121 <tests>
122 <test> 122 <test expect_num_outputs="1">
123 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> 123 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
124 <param name="mode_selector" value="correct" /> 124 <param name="mode_selector" value="correct" />
125 <param name='correctionMethod_selector' value='ice' /> 125 <param name="correctionMethod_selector" value="ice" />
126 <repeat name="chromosomes"> 126 <repeat name="chromosomes">
127 <param name="chromosome" value="chrUextra" /> 127 <param name="chromosome" value="chrUextra" />
128 </repeat> 128 </repeat>
129 <repeat name="chromosomes"> 129 <repeat name="chromosomes">
130 <param name="chromosome" value="chr3LHet" /> 130 <param name="chromosome" value="chr3LHet" />
131 </repeat> 131 </repeat>
132 <param name='filterThreshold_low' value='-2.0' /> 132 <param name="filterThreshold_low" value="-2.0" />
133 <param name='filterThreshold_large' value='4' /> 133 <param name="filterThreshold_large" value="4" />
134 <output name="outFileName" ftype="h5"> 134 <output name="outFileName" ftype="h5">
135 <assert_contents> 135 <assert_contents>
136 <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' /> 136 <has_h5_keys keys="correction_factors,intervals,matrix,nan_bins" />
137 </assert_contents> 137 </assert_contents>
138 </output> 138 </output>
139 </test> 139 </test>
140 <test> 140 <test expect_num_outputs="1">
141 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> 141 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
142 <param name="mode_selector" value="correct" /> 142 <param name="mode_selector" value="correct" />
143 <param name='correctionMethod_selector' value='kr' /> 143 <param name="correctionMethod_selector" value="kr" />
144 <output name="outFileName" ftype="h5"> 144 <output name="outFileName" ftype="h5">
145 <assert_contents> 145 <assert_contents>
146 <has_h5_keys keys='correction_factors,intervals,matrix' /> 146 <has_h5_keys keys="correction_factors,intervals,matrix" />
147 </assert_contents> 147 </assert_contents>
148 </output> 148 </output>
149 </test> 149 </test>
150 <test> 150 <test expect_num_outputs="1">
151 <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> 151 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
152 <param name="mode_selector" value="correct" /> 152 <param name="mode_selector" value="correct" />
153 <param name='correctionMethod_selector' value='kr' /> 153 <param name="correctionMethod_selector" value="kr" />
154 <output name="outFileName" ftype="cool"> 154 <output name="outFileName" ftype="cool">
155 <assert_contents> 155 <assert_contents>
156 <has_h5_keys keys='bins,chroms,indexes,pixels' /> 156 <has_h5_keys keys="bins,chroms,indexes,pixels" />
157 </assert_contents> 157 </assert_contents>
158 </output> 158 </output>
159 </test> 159 </test>
160 <test> 160 <test expect_num_outputs="1">
161 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> 161 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
162 162
163 <param name="mode_selector" value="correct" /> 163 <param name="mode_selector" value="correct" />
164 <param name='correctionMethod_selector' value='ice' /> 164 <param name="correctionMethod_selector" value="ice" />
165 <repeat name="chromosomes"> 165 <repeat name="chromosomes">
166 <param name="chromosome" value="chrUextra" /> 166 <param name="chromosome" value="chrUextra" />
167 </repeat> 167 </repeat>
168 <repeat name="chromosomes"> 168 <repeat name="chromosomes">
169 <param name="chromosome" value="chr3LHet" /> 169 <param name="chromosome" value="chr3LHet" />
170 </repeat> 170 </repeat>
171 <param name='filterThreshold_low' value='-2.0' /> 171 <param name="filterThreshold_low" value="-2.0" />
172 <param name='filterThreshold_large' value='4' /> 172 <param name="filterThreshold_large" value="4" />
173 <output name="outFileName" ftype="h5"> 173 <output name="outFileName" ftype="h5">
174 <assert_contents> 174 <assert_contents>
175 <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' /> 175 <has_h5_keys keys="correction_factors,intervals,matrix,nan_bins" />
176 </assert_contents> 176 </assert_contents>
177 </output> 177 </output>
178 </test> 178 </test>
179 <test> 179 <test expect_num_outputs="1">
180 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> 180 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
181 <param name="mode_selector" value="diagnostic_plot" /> 181 <param name="mode_selector" value="diagnostic_plot" />
182 <repeat name="chromosomes"> 182 <repeat name="chromosomes">
183 <param name="chromosome" value="chrUextra" /> 183 <param name="chromosome" value="chrUextra" />
184 </repeat> 184 </repeat>