Mercurial > repos > bgruening > hicexplorer_chicviewpointbackgroundmodel

annotate chicViewpointBackgroundModel.xml @ 3:7fe1a401d833 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 14:22:19 -0400
parents b9cdce1e57a1
children 628259b7ffb4
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1 <tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>compute a background model for cHi-C / HiChIP data</description>
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3 <macros>
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4 <token name="@BINARY@">chicViewpointBackgroundModel</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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15 @BINARY@
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17 --matrices $m
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18 --averageContactBin $averageContactBin
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19 --fixateRange $fixateRange
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20 --referencePoints '$referencePoints'
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21 $truncateZeros
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22 --threads @THREADS@
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23 --outFileName background.txt
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24 ]]></command>
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25 <inputs>
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26 <expand macro="matrix_h5_cooler_multiple_macro" />
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27
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28 <param argument="--referencePoints" type="data" format='interval'
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29 label="Reference points"
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30 help="Bed file contains all reference points which should be used to build the background model." />
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31 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
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32 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
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33 <param name='truncateZeros' type='boolean' truevalue='--truncateZeros' falsevalue="" checked="false" label="Truncate zeros"
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34 help="Set this parameter if you want truncate zeros to fight over dispersion."/>
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35 </inputs>
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36 <outputs>
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37 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
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42 <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
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43 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
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44 </test>
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45 <test>
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46 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
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47 <param name="truncateZeros" value="True"/>
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48 <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
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49 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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54 Compute a background model for cHi-C data analysis
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55 ==================================================
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57 chicViewpointBackgroundModel computes for all given samples with all reference points a background model. For all relative distances to a reference point
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58 a negative binomial distribution is fitted. Moreover, for each relative distance to a reference point the average value for this location is computed. Both
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59 background models are used, the first one for p-value and significance computation, the second one to filter out interactions with a less x-fold over mean.
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61 The background distributions are fixed at `--fixateRange` i.e. all distances lower / higher than this value use the fixed background distribution.
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63 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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64
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65 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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66 ]]></help>
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67 <expand macro="citations" />
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68 </tool>