Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix

annotate hicAdjustMatrix.xml @ 9:2e85fd0aa713 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author iuc
date Thu, 05 Dec 2024 17:41:27 +0000
parents 384a4cdc3c95
children
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9
2e85fd0aa713 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
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1 <tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>adjust the shape of a Hi-C matrix</description>
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3 <macros>
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4 <token name="@BINARY@">hicAdjustMatrix</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 #set matrix_name = 'matrix_in.' + str($matrix_h5_cooler.ext)
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10 #set matrix_file_out = 'matrix_out.' + str($matrix_h5_cooler.ext)
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11
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12 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
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13 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext'
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14 --action $action_selector
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15 --outFileName '$matrix_file_out'
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16 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionChromosomes":
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17 ## special: --chromosomeOrder is optional, but if given it needs at least one argument
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18 #set chroms = '\' \''.join([ str($var.chromosome) for $var in $chromosomeOrRegionFile_conditional.chromosomeOrder ])
ac2a7ed2de5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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19 #if chroms:
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20 --chromosomes '$chroms'
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21 #end if
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22 #end if
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23
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24 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile":
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25 --regions '$chromosomeOrRegionFile_conditional.regions'
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26 #end if
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27
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28 #if not $interIntra_selector == 'keep':
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29 --interIntraHandling $interIntra_selector
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30 #end if
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31 && mv '$matrix_file_out' matrix
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32
0
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33 ]]>
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34 </command>
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35 <inputs>
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36 <expand macro="matrix_h5_cooler_macro" />
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37 <param name="action_selector" type="select" label="Apply action">
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38 <option value="keep" selected="True">keep</option>
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39 <option value="remove">remove</option>
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40 <option value="mask">mask</option>
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41 </param>
ac2a7ed2de5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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42 <conditional name="chromosomeOrRegionFile_conditional">
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43 <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions">
ac2a7ed2de5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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44 <option value="optionChromosomes">Chromosomes</option>
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45 <option value="optionRegionFile" selected="True">Region BED file</option>
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46 </param>
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47 <when value="optionChromosomes">
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48 <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask" help="The selected option will be applied on the selected chromosomes.">
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49 <param name="chromosome" type="text">
0
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50 <validator type="empty_field" />
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51 </param>
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52 </repeat>
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53 </when>
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54 <when value="optionRegionFile">
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55 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" help="Should contain the regions which should be kept, removed or masked." />
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56 </when>
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57 </conditional>
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58 <param name="interIntra_selector" type="select" label="Remove inter- or intra chromosomal regions">
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59 <option value="keep" selected="True">Do not apply</option>
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60 <option value="inter">Remove inter-chromosomal contacts</option>
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61 <option value="intra">Remove intra-chromosomal contacts</option>
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62 </param>
0
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63 </inputs>
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64 <outputs>
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65 <data name="outFileName" from_work_dir="matrix" format="h5">
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66 <change_format>
0
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67 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
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68 </change_format>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <test expect_num_outputs="1">
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73 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
0
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74 <param name="action_selector" value="keep" />
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75 <conditional name="chromosomeOrRegionFile_conditional">
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76 <param name="chromosomeOrRegionFile_selector" value="optionChromosomes" />
0
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77 <repeat name="chromosomeOrder">
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78 <param name="chromosome" value="chrX" />
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79 <param name="chromosome" value="chr3R" />
0
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80 </repeat>
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81 </conditional>
ac2a7ed2de5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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82 <output name="outFileName" ftype="h5">
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83 <assert_contents>
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84 <has_h5_keys keys="intervals,matrix" />
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test expect_num_outputs="1">
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89 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
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90 <param name="action_selector" value="mask" />
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91 <conditional name="chromosomeOrRegionFile_conditional">
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92 <param name="chromosomeOrRegionFile_selector" value="optionRegionFile" />
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93 <param name="regions" value="regions.bed" />
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94 </conditional>
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95 <output name="outFileName" ftype="h5">
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96 <assert_contents>
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97 <has_h5_keys keys="intervals,matrix,nan_bins" />
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98 </assert_contents>
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99 </output>
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100 </test>
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101 </tests>
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102 <help><![CDATA[
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103
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104 Adjust of the Hi-C matrix
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105 =========================
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106
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107 This tool is able to remove, keep or mask given regions of a Hi-C interaction matrix, including entire chromosomes.
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108
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109 _________________
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110
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111 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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112
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113 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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114 ]]> </help>
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115 <expand macro="citations" />
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116 </tool>