Mercurial > repos > bgruening > hicexplorer_hictransform

annotate hicTransform.xml @ 2:40287e3ab12a draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
author iuc
date Wed, 03 Jan 2018 13:22:13 -0500
parents 5c869935cf2b
children 778158ebfddd
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2
40287e3ab12a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
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1 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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2 <description>transforms a matrix to a obs_exp, pearson and covariance matrix</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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9
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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">
40287e3ab12a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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29 <change_format>
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30 <when input="outputFormat" value="cool" format="cool" />
40287e3ab12a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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31 </change_format>
0
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32 </data>
2
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33 <data name="pearson" from_work_dir="pearson_matrix" format="h5">
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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>
0
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37 </data>
2
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38 <data name="covariance" from_work_dir="covariance_matrix" format="h5">
40287e3ab12a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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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>
0
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42 </data>
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43
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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"/>
0
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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.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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64 `hicTransform` computes three matrices: an observed/expected matrix based on it a
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65 pearson correlation matrix and based on it a covariance matrix. These three matrices
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66 can be used with `hicPlotMatrix` for an A / B compartment analysis.
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67
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68 Input
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69 -----
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70 - the matrix to be transformed
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71
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72 Parameters
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73 __________
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74 - Output file format: h5 or cool
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75
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76 Output
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77 ------
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78 - observed/expected matrix
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79 - pearson correlation matrix
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80 - covariance matrix.
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81
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82 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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83
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84 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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85 ]]></help>
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86 <expand macro="citations" />
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87 </tool>