Mercurial > repos > bgruening > hicexplorer_hicaverageregions

annotate hicAverageRegions.xml @ 2:4b6a36c18e5e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 17:05:58 -0400
parents d4aa0255c1eb
children 03d7978293fe
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f7c0aedd4be3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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1 <tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>sums Hi-C contacts around given reference points and computes their average.</description>
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3 <macros>
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4 <token name="@BINARY@">hicAverageRegions</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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11 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
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12 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext'
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f7c0aedd4be3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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14 --regions '$regions'
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15 #if $rangeFormat_conditional.rangeFormat_selector == 'optionGenomicUnits':
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16 --range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
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17 #else:
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18 --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
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19 #end if
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20 --coordinatesToBinMapping $coordinatesToBinMapping_selector
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21 --outFileName output_matrix.npz
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23 ]]>
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24 </command>
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25 <inputs>
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26 <expand macro='matrix_h5_cooler_macro' />
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27 <param argument="--regions" type="data" format='bed'
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28 label="Regions to average"
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29 help="BED file which stores a list of regions that are summed and averaged."/>
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30
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31 <conditional name="rangeFormat_conditional">
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32 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
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33 <option value="optionGenomicUnits">Range in genomic units</option>
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34 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option>
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35 </param>
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36 <when value="optionGenomicUnits">
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37 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
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38 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
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39 </when>
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40 <when value="optionBinUnits">
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41 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
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42 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
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43 </when>
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44 </conditional>
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45 <param name="coordinatesToBinMapping_selector" type="select" label="Define start value of range" help="If the region contains start and end coordinates, define if the start, center (start + (end-start) / 2) or end bin should be used as start for range.">
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46 <option value="start">Start</option>
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47 <option value="center" selected="True">Center</option>
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48 <option value="end" selected="True">End</option>
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49 </param>
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50 </inputs>
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51 <outputs>
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52 <data name="outFileName" from_work_dir="output_matrix.npz" format="zip"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
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57 <param name="regions" value="hicAverageRegions/regions.bed" />
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58 <conditional name="rangeFormat_conditional">
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59 <param name="rangeFormat_selector" value='optionGenomicUnits'/>
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60 <param name="upstreamRange" value='100000'/>
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61 <param name="downstreamRange" value='100000'/>
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62 </conditional>
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63
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64 <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" />
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65 </test>
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66 <test>
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67 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
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68 <param name="regions" value="hicAverageRegions/regions.bed" />
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69 <conditional name="rangeFormat_conditional">
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70 <param name="rangeFormat_selector" value='optionBinUnits'/>
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71 <param name="upstreamRange" value='100'/>
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72 <param name="downstreamRange" value='100'/>
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73 </conditional>
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75 <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" />
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79
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80 Average regions
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81 ===============
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82
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83 This tool sums Hi-C contacts around given reference points and computes their average. This tool is useful to detect differences at certain reference points, TAD boundaries for instance, between samples.
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85 WARNING: This tool can only be used with fixed bin size Hi-C matrices. No guarantees how and if it works on restriction site interaction matrices.
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87 Use the output to plot the average with hicPlotAverageRegions.
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89 _________________
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91 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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93 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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94 ]]></help>
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95 <expand macro="citations" />
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96 </tool>