Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

annotate hicCompareMatrices.xml @ 0:a0ab04565c73 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:37:57 -0500
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children 08e157ceda6f
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a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>normalize and compare two HiC matricies</description>
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3 <macros>
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4 <token name="@BINARY@">hicCompareMatrices</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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10 @BINARY@
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11 --matrices '$matrix1' '$matrix2'
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12 --operation $operation
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13 --outFileName matrix.$outputFormat
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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14
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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15 && mv matrix.$outputFormat matrix
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name='matrix1' type="data" format="h5,cool"
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20 label="First matrix"/>
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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21 <param name='matrix2' type="data" format="h5,cool"
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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22 label="Second matrix to compare against the first"/>
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23
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24 <param name='operation' type='select' label="Operation to be used for the comparison">
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25 <option value='diff'>diff</option>
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26 <option value="ratio">ratio</option>
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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27 <option value="log2ratio">log2ratio</option>
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28 </param>
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29 <param name='outputFormat' type='select' label="Output file format">
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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30 <option value='h5'>HiCExplorer format</option>
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31 <option value="cool">cool</option>
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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32 </param>
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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33 </inputs>
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34 <outputs>
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35 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
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36 <change_format>
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37 <when input="outputFormat" value="cool" format="cool" />
a0ab04565c73 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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38 </change_format>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="matrix1" value="small_test_matrix.h5"/>
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44 <param name="matrix2" value="small_test_matrix.h5"/>
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45 <param name="operation" value='log2ratio' />
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46 <param name="outputFormat" value="h5" />
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47 <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/>
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48 </test>
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49 <test>
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50 <param name="matrix1" value="pearson_small_50kb.cool"/>
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51 <param name="matrix2" value="pearson_small_50kb.cool"/>
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52 <param name="operation" value='ratio' />
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53 <param name="outputFormat" value="cool" />
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54 <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/>
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55 </test>
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56
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57 </tests>
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58 <help><![CDATA[
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59 Comparison of HiC matrices
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60 ==========================
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61 `hicCompareMatrices` takes two matrices, normalizes them and appliesthe given operation. To
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62 normalize the matrices each element is divided by sum of the matrix.
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63
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64 Input
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65 -----
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66 - the matricies to be compared
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67
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68
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69
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70 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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71
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72 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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73 ]]></help>
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74 <expand macro="citations" />
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75 </tool>