Mercurial > repos > bgruening > hicexplorer_chicviewpointbackgroundmodel

annotate chicViewpointBackgroundModel.xml @ 7:b285586b61a6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
author iuc
date Tue, 10 Jan 2023 18:54:10 +0000
parents 628259b7ffb4
children 9d02f1819e81
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1 <tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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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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.$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
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15 @BINARY@
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16 --matrices $m
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17 --averageContactBin $averageContactBin
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18 --fixateRange $fixateRange
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19 --referencePoints '$referencePoints'
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20 $truncateZeros
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21 --threads @THREADS@
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22 --outFileName background.txt
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23 ]]> </command>
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24 <inputs>
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25 <expand macro="matrix_h5_cooler_multiple_macro" />
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26 <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
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27 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' />
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28 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' />
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29 <param argument='--truncateZeros' type='boolean' truevalue='--truncateZeros' falsevalue="" checked="false" label="Truncate zeros" help="Set this parameter if you want truncate zeros to fight over dispersion." />
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30 </inputs>
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31 <outputs>
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32 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model" />
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33 </outputs>
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34 <tests>
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35 <test expect_num_outputs="1">
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36 <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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37 <param name="referencePoints" value="cHi-C/referencePoints.bed" />
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38 <output name="background" ftype="tabular">
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39 <assert_contents>
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40 <has_text text="-500000" />
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41 <has_text text="-498000" />
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42 <has_n_columns n="5" />
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43 <has_text text="nbinom" />
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44 </assert_contents>
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45 </output>
3
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46 </test>
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47 <test expect_num_outputs="1">
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48 <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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49 <param name="truncateZeros" value="True" />
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50 <param name="referencePoints" value="cHi-C/referencePoints.bed" />
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51 <output name="background" ftype="tabular">
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52 <assert_contents>
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53 <has_text text="476000" />
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54 <has_text text="491000" />
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55 <has_n_columns n="5" />
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56 <has_text text="nbinom" />
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57 </assert_contents>
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58 </output>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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63 Compute a background model for cHi-C data analysis
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64 ==================================================
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66 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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67 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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68 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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69
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70 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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72 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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74 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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75 ]]> </help>
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76 <expand macro="citations" />
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77 </tool>