Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

annotate hicBuildMatrix.xml @ 0:9767c021cd58 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:30:47 -0400
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children eb0d14cdf8b8
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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2 <description>creates a matrix of interactions</description>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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3 <macros>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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4 <token name="@BINARY@">hicBuildMatrix</token>
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5 <import>macros.xml</import>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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6 </macros>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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7 <expand macro="requirements" >
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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8 <requirement type="package" version="1.3.1">samtools</requirement>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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9 </expand>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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10 <command>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 <![CDATA[
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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13 mkdir ./QCfolder &&
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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14 mkdir $qc.files_path
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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15 &&
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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16
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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17 hicBuildMatrix
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18
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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19 --samFiles
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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20 #for $repeat in $samFiles:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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21 '${repeat.samFile}'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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22 #end for
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23
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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24 #if $binSize:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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25 --binSize $binSize
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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26 #end if
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27
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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28 #if $restrictionCutFile:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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29 --restrictionCutFile '$restrictionCutFile'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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30 #end if
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31
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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32 #if $minDistance:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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33 --minDistance $minDistance
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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34 #end if
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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35
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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36 #if $maxDistance:
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37 --maxDistance $maxDistance
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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38 #end if
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39
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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40 #if $restrictionSequence:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41 --restrictionSequence '$restrictionSequence'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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42 #end if
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43
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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44 #if $region:
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45 --region '$region'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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46 #end if
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47
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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48 --outFileName ./matrix.h5
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49 --outBam ./unsorted.bam
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50
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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51 #if $restrictionCutFile:
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52 --restrictionCutFile '$restrictionCutFile'
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53 #end if
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54
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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55 $removeSelfCircles
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56
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57 #if $minMappingQuality and $minMappingQuality is not None:
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58 --minMappingQuality $minMappingQuality
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59 #end if
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60
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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61 --QCfolder ./QCfolder
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62 &&
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63 mv ./QCfolder/* $qc.files_path/
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64 &&
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65 mv $qc.files_path/hicQC.html $qc
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66 &&
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67 samtools sort ./unsorted.bam -o sorted.bam
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68
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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69 ]]>
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70 </command>
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71 <inputs>
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72 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">
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73 <param name="samFile" type="data" format="sam,bam"/>
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74 </repeat>
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75
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76 <param argument="--restrictionCutFile" type="data" format="bed" optional="True"
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77 help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
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78 bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>
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79
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80 <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp"
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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81 help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
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82 Otherwise all reads in the interval are considered. " argument="--binSize"/>
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83
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84 <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
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85 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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86 (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/>
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87
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88 <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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89 help="Restriction sites that are closer that this distance are merged into one.
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90 This option only applies if --restrictionCutFile is given." argument="--minDistance"/>
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91
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92 <param name="maxDistance" type="integer" value="" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one"
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93 help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/>
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94
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95 <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
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96 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
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97 &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/>
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98
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99 <expand macro="region" />
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100
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101 <param argument="--removeSelfCircles" type="boolean" truevalue="--removeSelfCircles" falsevalue=""
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102 label="Save the matrix of values underlying the heatmap" help="If set, outward facing reads, at a distance of less thatn 25kbs are removed." />
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103
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104 <expand macro="minMappingQuality" />
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105
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106 </inputs>
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107 <outputs>
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108 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
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109 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
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110 <data name="qc" format="html" label="${tool.name} QC"/>
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111 </outputs>
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112 <tests>
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113 <test>
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114 <repeat name="samFiles">
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115 <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
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116 </repeat>
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117 <repeat name="samFiles">
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118 <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
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119 </repeat>
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120 <param name="binSize" value="5000"/>
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121 <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/>
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122 <output name="outFileName" file="hicBuildMatrix_result1.h5" ftype="h5" compare="sim_size"/>
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123 </test>
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124 </tests>
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125 <help><![CDATA[
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126
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127 **What it does**
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128
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129 Creates a matrix of interactions.
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130
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131 ]]></help>
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132 <expand macro="citations" />
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133 </tool>