Mercurial > repos > bgruening > hicexplorer_hiccompartmentspolarization
annotate hicCompartmentsPolarization.xml @ 0:8d764e8acdf5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 17:26:46 -0500 |
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8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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1 <tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@WRAPPER_VERSION@.0"> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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3 <macros> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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4 <token name="@BINARY@">hicCompartmentsPolarization</token> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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5 <import>macros.xml</import> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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6 </macros> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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7 <expand macro="requirements" /> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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8 <command detect_errors="exit_code"><![CDATA[ |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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9 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple): |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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11 ln -s '$m' '${counter}_matrix.$m.ext' && |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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12 #end for |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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14 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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15 @BINARY@ |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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16 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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17 --obsexp_matrices $m |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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18 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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19 --pca '$pca' |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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20 ##--quantile #echo int($quantile) # |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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21 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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22 $outputMatrix |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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23 ##--outliers #echo float($outliers) # |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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24 --outputFileName plot.$image_file_format |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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25 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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26 && mv plot.$image_file_format plot |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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27 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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28 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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29 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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30 ]]> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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31 </command> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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32 <inputs> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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33 <expand macro="matrix_h5_cooler_multiple_macro" /> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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34 <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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35 no header. In case of several matrices with |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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36 different conditions, ie. control |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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37 treatment, the PCA of control can be |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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38 used. Note that only one PCA can be provided.'/> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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39 <!-- <param name='quantile' type="integer" label="Quantile" help='The number of to be used quantiles.' value="30"/> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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40 <param name='outliers' type="float" label="Outliers" help='The number of outliers to be removed.' value="0.0"/> --> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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41 <param name='outputMatrix' type='boolean' optional="true" truevalue='--outputMatrix output_matrix.npz' falsevalue='' label='Return computed matrix' help='Output .npz file includes all the generated matrices' /> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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42 <param name="image_file_format" type="select" label="Image output format"> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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43 <option value="png" selected="True">png</option> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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44 <option value="svg">svg</option> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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45 <option value="pdf">pdf</option> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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46 </param> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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47 </inputs> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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48 <outputs> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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49 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot"> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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50 <change_format> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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51 <when input="image_file_format" value="svg" format="svg" /> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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52 <when input="image_file_format" value="pdf" format="pdf" /> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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53 </change_format> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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54 </data> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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55 <data name='output_matrix' from_work_dir='output_matrix.npz' format='hicexplorer_compartments_matrix' label='Output .npz file includes all the generated matrices'> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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56 <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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57 </data> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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58 </outputs> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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59 <tests> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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60 <test> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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61 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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62 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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63 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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64 </test> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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65 </tests> |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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66 <help><![CDATA[ |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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67 |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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68 Matrix correlation |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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69 ================== |
8d764e8acdf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2-dirty"
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70 |
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71 **hicCorrelate** is a dedicated Quality Control tool that allows the correlation of multiple Hi-C matrices at once with either a heatmap or scatterplots output. |
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72 |
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73 Computes pairwise correlations between Hi-C matrices data. The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices. Parameters that strongly affect correlations are bin size of the Hi-C matrices (can be changed using ``hicMergeMatrixBins``) and the considered range. The smaller the bin size of the matrices, the finer the differences you score. The *Range* parameter should be selected at a meaningful genomic scale according to, for example, the mean size of the TADs in the organism you work with or to specific ranges found using ``hicPlotDistVsCounts``. |
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74 |
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75 _________________ |
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76 |
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77 Usage |
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78 ----- |
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79 |
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80 It is recommended to use this tool on corrected matrices (``hicCorrectMatrix``) at restriction enzyme resolution (unmerged bins). |
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81 |
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82 _________________ |
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83 |
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84 Output |
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85 ------ |
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86 |
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87 **hicCorrelate** outputs correlation plots of multiple Hi-C matrices. |
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88 |
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89 Below, you can find a correlation example of uncorrected Hi-C matrices obtained from *Drosophila melanogaster* embryos, either wild-type or having one gene knocked-down by RNAi. |
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90 |
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91 Heatmap |
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92 _______ |
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93 |
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94 .. image:: $PATH_TO_IMAGES/hicCorrelate_Dmel_heatmap.png |
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95 :width: 45% |
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96 |
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97 This example is showing a heatmap that was calculated using the Pearson correlation of corrected Hi-C matrices with a bin size of 6000 bp at a range of 5000 to 200000. The dendrogram indicates which samples are most similar to each other. You can see that the wild-type samples are seperated from the knock-down samples. In that case, Spearman correlation gives very similar results (not shown). |
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98 |
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99 Scatterplot |
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100 ___________ |
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101 |
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102 .. image:: $PATH_TO_IMAGES/hicCorrelate_Dmel_scatterplot.png |
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103 :width: 45% |
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104 |
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105 Additionally, pairwise scatterplots comparing interactions between each sample can be plotted. |
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106 |
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107 _________________ |
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108 |
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109 For more information about HiCExplorer please consider our documentation on readthedocs.io_. |
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110 |
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111 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
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112 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html |
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113 |
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114 ]]></help> |
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115 <expand macro="citations" /> |
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116 </tool> |