Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate hicSumMatrices.xml @ 4:d387dacb6867 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:35:53 -0500
parents 2bbe234ca6ce
children b9f41afc3312
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c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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3 <macros>
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4 <token name="@BINARY@">hicSumMatrices</token>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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5 <import>macros.xml</import>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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, $m in enumerate($matrices):
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 ln -s '$m' ${counter}.npz.h5 &&
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 #end for
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13
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14 #set $m = '" "'.join([ '%s.npz.h5' % $counter for $counter, $matrix in enumerate($matrices) ])
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15 hicSumMatrices
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16 --matrices "$m"
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17 --outFileName ./out.npz.h5
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param argument="--matrices" type="data" format="h5" multiple="True"
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22 label="Matrices to combine" help="Needs to have the same shape"/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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23 </inputs>
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24 <outputs>
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25 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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26 </outputs>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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27 <tests>
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28 <test>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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29 <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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30 <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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31 </test>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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32 </tests>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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33 <help><![CDATA[
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d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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34 Summation of matrices
d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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35 =====================
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36
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d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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37 ``hicSumMatrix`` is combining two (or more) contact matrices of the same size to one.
d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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38 This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to
d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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39 increase the power of the data. It is the nature of Hi-C that real contact cannot be distinguished
d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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40 from noise, especially with a low contact count. The more contacts are given, the more likely it is
d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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41 that a high number of contacts are real contact or contain at least a high amount. Therefore it is
d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
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42 a common way to merge replicates of Hi-C experiments to increase the validity of the experiment.
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43
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44 Input
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45 -----
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46
d387dacb6867 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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47 Parameters
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48 __________
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49 - two or matrices of the same shape.
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50
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51 Output
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52 ------
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53 The summed matrix.
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54
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55 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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56
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57 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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58 ]]></help>
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59 <expand macro="citations" />
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60 </tool>