annotate hicTransform.xml @ 4:d5bf6e7d3800 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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date Fri, 27 Apr 2018 03:34:37 -0400
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1 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>transform a matrix to obs/exp, pearson and covariance matrices</description>
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3 <macros>
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4 <token name="@BINARY@">hicTransform</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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11 hicTransform --matrix '$matrix_h5_cooler'
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12 --method all
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13 --outFileName matrix.$outputFormat
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14 && mv obs_exp_matrix.$outputFormat obs_exp_matrix
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15 && mv pearson_matrix.$outputFormat pearson_matrix
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16 && mv covariance_matrix.$outputFormat covariance_matrix
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17 ]]>
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18 </command>
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19 <inputs>
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20 <expand macro='matrix_h5_cooler_macro' />
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21 <param name='outputFormat' type='select' label="Output file format">
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22 <option value='h5'>HiCExplorer format</option>
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23 <option value="cool">cool</option>
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24 </param>
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25
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26 </inputs>
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27 <outputs>
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28 <data name="obs_exp" from_work_dir="obs_exp_matrix" format="h5" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Observed/Expected matrix">
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29 <change_format>
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30 <when input="outputFormat" value="cool" format="cool"/>
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31 </change_format>
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32 </data>
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33 <data name="pearson" from_work_dir="pearson_matrix" format="h5" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Pearson matrix">
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34 <change_format>
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35 <when input="outputFormat" value="cool" format="cool"/>
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36 </change_format>
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37 </data>
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38 <data name="covariance" from_work_dir="covariance_matrix" format="h5" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Covariance matrix">
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39 <change_format>
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40 <when input="outputFormat" value="cool" format="cool"/>
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41 </change_format>
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42 </data>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
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48 <param name="outputFormat" value="h5" />
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49 <output name="obs_exp" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/>
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50 <output name="pearson" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/>
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51 <output name="covariance" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/>
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52 </test>
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53 <test>
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54 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
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55 <param name="outputFormat" value="cool" />
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56 <output name="obs_exp" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/>
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57 <output name="pearson" file="pearson_small_50kb_transform.cool" ftype="cool" compare="sim_size"/>
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58 <output name="covariance" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 Transformation of matrix for plotting
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63 =====================================
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65 **hicTransform** computes three matrices based on one Hi-C contact matrix as input based on the methods determined by `Lieberman-Aiden et al. (2009)`_:
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66
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67 - An **observed/expected matrix** obtained "by dividing each entry in the contact matrix by the genome-wide average contact probability for loci at that genomic distance" (`Lieberman-Aiden et al. (2009)`_). This transformation allows to better assess long range interactions.
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68 - A **Pearson correlation matrix** obtained by computing the Pearson correlation between each bin based on observed/expected values. This matrix transformation allows to better identify the bins that are entering in contact together, or not, at long ranges, and thus helps defining compartments in the nucleus (``hicPCA``).
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69 - A **covariance matrix**, which is used as a basis for the Principal Component Analysis (PCA) to compute the eigenvectors outputed by **hicTransform**.
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70
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71 These three matrices can be used with ``hicPlotMatrix`` or ``hicPlotTADs`` for a visualization of the A / B compartment analysis.
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73 _________________
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75 Output
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76 ------
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78 From one Hi-C contact matrix, **hicTransform** outputs the observed/expected, Pearson correlation and covariance matrices.
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80 _________________
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82 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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84 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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85 .. _`Lieberman-Aiden et al. (2009)`: https://dx.doi.org/10.1126%2Fscience.1181369
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86 ]]></help>
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87 <expand macro="citations" />
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88 </tool>