Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate hicSumMatrices.xml @ 9:0399cd2c25aa draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:31:58 -0400
parents c109622e0cf5
children e89bc5e38823
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1 <tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>combine Hi-C matrices of the same size</description>
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3 <macros>
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4 <token name="@BINARY@">hicSumMatrices</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 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
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11 ln -s '$m' ${counter}_matrix &&
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12 #end for
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13 #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
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15 hicSumMatrices
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16 --matrices "$m"
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17 --outFileName matrix.$outputFormat
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19 && mv matrix.$outputFormat matrix
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20 ]]>
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21 </command>
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22 <inputs>
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23 <expand macro='matrix_h5_cooler_multiple_macro'/>
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24
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25 <param name='outputFormat' type='select' label="Output file format">
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26 <option value='h5'>HiCExplorer format</option>
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27 <option value="cool">cool</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="outFileName" from_work_dir="matrix" format="h5">
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32 <change_format>
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33 <when input="outputFormat" value="cool" format="cool" />
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34 </change_format>
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35 </data>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
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40 <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> -->
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41 <param name='outputFormat' value='h5'/>
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42 <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 Summation of matrices
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47 =====================
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49 **hicSumMatrix** is combining two (or more) contact matrices of the same size to one.
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50 This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to
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51 increase the coverage of the data. With Hi-C, real contacts are sometimes difficult to be distinguished
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52 from noise, especially with a low contact count. The more contacts are given, the more likely it is
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53 that a high number of contacts are biologically releveant. It is therefore common to merge biological
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54 and technical replicates of Hi-C experiments and **hicSumMatrix** address this concern.
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56 _________________
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58 Usage
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59 -----
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61 This tool takes two or more Hi-C contact matrices and sum the contacts into one matrix. It is recommended to use uncorrected and unmerged matrices as input (use the direct output from ``hicBuildMatrix``). Bin merging (``hicMergeMatrixBins``) and Hi-C contact matrix correction (``hicCorrectMatrix``) must be performed afterwards.
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63 _________________
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65 Output
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66 ------
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67 **hicSumMatrix** outputs a Hi-C contact matrix comprising the sum of all the contacts of the Hi-C matrices used as input.
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69 _________________
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71 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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73 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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74 ]]></help>
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75 <expand macro="citations" />
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76 </tool>