Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate hicSumMatrices.xml @ 17:5fbf0fd998ce draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 05:36:54 -0400
parents e89bc5e38823
children 5aa5ef83f975
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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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10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
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11 ln -s '$m' '${counter}_matrix.$m.ext' &&
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12 #end for
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13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
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14 #set $extension = $matrix_h5_cooler_multiple[0].ext
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15 @BINARY@
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16 --matrices $m
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17 --outFileName 'matrix.$extension'
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18
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19 && mv 'matrix.$extension' 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 </inputs>
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25 <outputs>
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26 <data name="outFileName" from_work_dir="matrix" format_source='matrix_h5_cooler_multiple'/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
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32 <output name="outFileName" ftype="h5">
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33 <assert_contents>
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34 <has_h5_keys keys='intervals,matrix'/>
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35 </assert_contents>
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36 </output>
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37 </test>
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38 <test>
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39 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>
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41 <output name="outFileName" ftype="cool">
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42 <assert_contents>
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43 <has_h5_keys keys='bins,chroms,indexes,pixels'/>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 Summation of matrices
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50 =====================
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51
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52 **hicSumMatrix** is combining two (or more) contact matrices of the same size to one.
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53 This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to
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54 increase the coverage of the data. With Hi-C, real contacts are sometimes difficult to be distinguished
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55 from noise, especially with a low contact count. The more contacts are given, the more likely it is
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56 that a high number of contacts are biologically releveant. It is therefore common to merge biological
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57 and technical replicates of Hi-C experiments and **hicSumMatrix** address this concern.
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58
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59 _________________
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61 Usage
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62 -----
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64 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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66 _________________
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67
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68 Output
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69 ------
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70 **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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72 _________________
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74 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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76 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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77 ]]></help>
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78 <expand macro="citations" />
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79 </tool>