Mercurial > repos > bgruening > hicexplorer_hicaverageregions

annotate hicAverageRegions.xml @ 0:f7c0aedd4be3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:21:06 -0500
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children d4aa0255c1eb
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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 --outFileName output_matrix.npz
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21
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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_macro' />
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26 <param argument="--regions" type="data" format='bed'
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27 label="Regions to average"
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28 help="BED file which stores a list of regions that are summed and averaged."/>
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29
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30 <conditional name="rangeFormat_conditional">
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31 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
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32 <option value="optionGenomicUnits">Range in genomic units</option>
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33 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option>
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34 </param>
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35 <when value="optionGenomicUnits">
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36 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
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37 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
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38 </when>
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39 <when value="optionBinUnits">
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40 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
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41 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data name="outFileName" from_work_dir="output_matrix.npz" format="zip"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
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51 <param name="regions" value="hicAverageRegions/regions.bed" />
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52 <conditional name="rangeFormat_conditional">
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53 <param name="rangeFormat_selector" value='optionGenomicUnits'/>
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54 <param name="upstreamRange" value='100000'/>
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55 <param name="downstreamRange" value='100000'/>
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56 </conditional>
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57
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58 <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" />
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59 </test>
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60 <test>
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61 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
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62 <param name="regions" value="hicAverageRegions/regions.bed" />
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63 <conditional name="rangeFormat_conditional">
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64 <param name="rangeFormat_selector" value='optionBinUnits'/>
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65 <param name="upstreamRange" value='100'/>
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66 <param name="downstreamRange" value='100'/>
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67 </conditional>
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68
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69 <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" />
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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74 Average regions
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75 ===============
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76
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77 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 as for example TAD boundaries between samples.
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78
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79 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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80
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81 Use the output to plot the average with hicPlotAverageRegions.
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82
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83 _________________
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85 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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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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87 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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88 ]]></help>
f7c0aedd4be3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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89 <expand macro="citations" />
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90 </tool>