Mercurial > repos > bgruening > hicexplorer_hicaggregatecontacts
comparison hicAggregateContacts.xml @ 5:ce16a538ab46 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 15:27:02 -0500 |
parents | 2abdd761461b |
children | ee370ade24cd |
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4:0c812ed34277 | 5:ce16a538ab46 |
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5 <token name="@BINARY@">hicAggregateContacts</token> | 5 <token name="@BINARY@">hicAggregateContacts</token> |
6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
7 </macros> | 7 </macros> |
8 <expand macro="requirements" /> | 8 <expand macro="requirements" /> |
9 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
10 @BINARY@ | 10 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && |
11 --matrix '$matrix_h5_cooler' | 11 @BINARY@ |
12 --matrix 'matrix.$matrix_h5_cooler.ext' | |
12 --BED $BED | 13 --BED $BED |
13 #if $BED2: | 14 #if $BED2: |
14 --BED2 $BED2 | 15 --BED2 $BED2 |
15 #end if | 16 #end if |
16 | 17 |
17 --range $range_min:$range_max | 18 --range '$range_min:$range_max' |
18 | 19 |
19 --numberOfBins $numberOfBins | 20 --numberOfBins '$numberOfBins' |
20 | 21 |
21 --transform $transform | 22 --transform $transform |
22 --avgType $avgType | 23 --avgType $avgType |
23 | 24 |
24 #if $outputs and 'PrefixMatrix' in $outputs: | 25 #if $outputs and 'PrefixMatrix' in $outputs: |
126 help= "Maximum value of the plotted score." /> | 127 help= "Maximum value of the plotted score." /> |
127 | 128 |
128 <param name="image_file_format" type="select" label="Image output format"> | 129 <param name="image_file_format" type="select" label="Image output format"> |
129 <option value="png" selected="True">png</option> | 130 <option value="png" selected="True">png</option> |
130 <option value="svg">svg</option> | 131 <option value="svg">svg</option> |
132 <option value="pdf">pdf</option> | |
133 | |
131 </param> | 134 </param> |
132 | 135 |
133 <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files"> | 136 <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files"> |
134 <option value="PrefixMatrix">Save values underlying the final matrix</option> | 137 <option value="PrefixMatrix">Save values underlying the final matrix</option> |
135 <option value="ClusterContactPositions">Save the position of the contacts</option> | 138 <option value="ClusterContactPositions">Save the position of the contacts</option> |
139 </inputs> | 142 </inputs> |
140 <outputs> | 143 <outputs> |
141 <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot"> | 144 <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot"> |
142 <change_format> | 145 <change_format> |
143 <when input="image_file_format" value="svg" format="svg" /> | 146 <when input="image_file_format" value="svg" format="svg" /> |
147 <when input="image_file_format" value="pdf" format="pdf" /> | |
148 | |
144 </change_format> | 149 </change_format> |
145 </data> | 150 </data> |
146 <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values"> | 151 <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values"> |
147 <discover_datasets pattern="matrix_values_(?P<designation>.*)\..*" directory="./" format="tabular" /> | 152 <discover_datasets pattern="matrix_values_(?P<designation>.*)\..*" directory="./" format="tabular" /> |
148 </collection> | 153 </collection> |
153 <discover_datasets pattern="heatmap_(?P<designation>.*)\..*" directory="./" format="tabular" /> | 158 <discover_datasets pattern="heatmap_(?P<designation>.*)\..*" directory="./" format="tabular" /> |
154 </collection> | 159 </collection> |
155 </outputs> | 160 </outputs> |
156 <tests> | 161 <tests> |
157 <test> | 162 <test> |
158 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/> | 163 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool"/> |
159 <param name="BED" value="test_regions.bed" ftype="bed"/> | 164 <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed"/> |
160 <param name="numberOfBins" value="30" /> | 165 <param name="numberOfBins" value="30" /> |
161 <param name="range_max" value="900000" /> | 166 <param name="range_max" value="900000" /> |
162 <param name="range_min" value="50000" /> | 167 <param name="range_min" value="50000" /> |
163 <param name="image_file_format" value="png" /> | 168 <param name="image_file_format" value="png" /> |
164 <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" /> | 169 <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" delta='35000'/> |
165 </test> | 170 </test> |
166 </tests> | 171 </tests> |
167 <help><![CDATA[ | 172 <help><![CDATA[ |
168 Aggregation of Hi-C contacts | 173 Aggregation of Hi-C contacts |
169 ============================ | 174 ============================ |