Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate hicSumMatrices.xml @ 5:b9f41afc3312 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:36:36 -0500
parents d387dacb6867
children e0df60f3b0d5
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1 <tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>combines 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 #if $outputFormat == 'h5'
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18 --outFileName matrix.h5
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19 #elif $outputFormat == 'cool'
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20 --outFileName matrix.cool
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21 #end if
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22 ]]>
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23 </command>
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24 <inputs>
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25 <expand macro='matrix_h5_cooler_multiple_macro'/>
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27 <param name='outputFormat' type='select' label="Output file format">
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28 <option value='h5'>HiCExplorer format</option>
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29 <option value="cool">cool</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5">
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34 <filter>outputFormat == 'h5'</filter>
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35 </data>
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36 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool">
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37 <filter>outputFormat == 'cool'</filter>
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38 </data>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
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43 <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> -->
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44 <param name='outputFormat' value='h5'/>
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45 <output name="outFileName_h5" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
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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 power of the data. It is the nature of Hi-C that real contact cannot 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 real contact or contain at least a high amount. Therefore it is
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57 a common way to merge replicates of Hi-C experiments to increase the validity of the experiment.
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58
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59 Input
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60 -----
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61
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62 Parameters
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63 __________
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64 - two or matrices of the same shape.
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65
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66 Output
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67 ------
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68 The summed matrix.
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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>