Mercurial > repos > bgruening > hicexplorer_hicaverageregions

annotate hicAverageRegions.xml @ 8:c72fa6cb8817 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 11:10:09 +0000
parents b15d27c440fd
children
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1 <tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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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10 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
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11 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext'
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13 --regions '$regions'
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14 #if $rangeFormat_conditional.rangeFormat_selector == 'optionGenomicUnits':
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15 --range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
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16 #else:
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17 --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
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18 #end if
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19 --coordinatesToBinMapping $coordinatesToBinMapping_selector
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20 $considerStrandDirection
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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" label="Regions to average" help="BED file which stores a list of regions that are summed and averaged." />
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28
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29 <conditional name="rangeFormat_conditional">
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30 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
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31 <option value="optionGenomicUnits">Range in genomic units</option>
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32 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option>
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33 </param>
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34 <when value="optionGenomicUnits">
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35 <param name="upstreamRange" type="integer" value="" label="Upstream range" />
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36 <param name="downstreamRange" type="integer" value="" label="Downstream range" />
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37 </when>
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38 <when value="optionBinUnits">
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39 <param name="upstreamRange" type="integer" value="" label="Upstream range" />
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40 <param name="downstreamRange" type="integer" value="" label="Downstream range" />
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41 </when>
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42 </conditional>
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43 <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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44 <option value="start">Start</option>
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45 <option value="center" selected="True">Center</option>
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46 <option value="end" selected="True">End</option>
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47 </param>
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48 <param argument="--considerStrandDirection" type="boolean" truevalue="--considerStrandDirection" falsevalue="" label="Consider strand direction" help="This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1]." />
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49
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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" ftype="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 <output name="outFileName" file="hicAverageRegions/result_range_100000.npz" ftype="zip" compare="sim_size" delta="20000" />
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64 </test>
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65 <test>
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66 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
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67 <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed" />
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68 <conditional name="rangeFormat_conditional">
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69 <param name="rangeFormat_selector" value="optionBinUnits" />
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70 <param name="upstreamRange" value="100" />
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71 <param name="downstreamRange" value="100" />
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72 </conditional>
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73 <output name="outFileName" file="hicAverageRegions/result_rangeInBins_100.npz" ftype="zip" compare="sim_size" delta="20000" />
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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78 Average regions
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79 ===============
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81 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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83 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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85 Use the output to plot the average with hicPlotAverageRegions.
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87 _________________
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89 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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91 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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92 ]]> </help>
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93 <expand macro="citations" />
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94 </tool>