Mercurial > repos > bgruening > bionano_scaffold

annotate test-data/configuration.xml @ 0:fec6a0b53189 draft

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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
author bgruening
date Mon, 17 May 2021 15:07:05 +0000
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fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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1 <hybridScaffold>
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2 <version>
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3 <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/>
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4 </version>
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5 <global>
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6 <flag attr="maxmem" val0="960" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>
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7 <flag attr="maxthreads" val0="54" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
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8 <flag attr="maxvirtmem" val0="960"/>
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9 <flag attr="RAmem" val0="3" val1="1"/>
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10 </global>
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11 <fasta2cmap>
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12 <flag attr="enzyme" val0="BspQI" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
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13 <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
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14 <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
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15 <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
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16 </fasta2cmap>
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17 <align0>
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18 <flag attr="M" val0="1" val1="3"/>
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19 <flag attr="ScaleDelta" val0="0.02" val1="15"/>
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20 <flag attr="ScaleDeltaBPP"/>
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21 <flag attr="hashScaleDelta" val0="2"/>
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22 <flag attr="res" val0="2.9"/>
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23 <flag attr="FP" val0="0.6"/>
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24 <flag attr="FN" val0="0.06"/>
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25 <flag attr="sf" val0="0.20"/>
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26 <flag attr="sd" val0="0.0"/>
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27 <flag attr="sr" val0="0.01"/>
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28 <flag attr="extend" val0="1"/>
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29 <flag attr="outlier" val0="0.0001"/>
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30 <flag attr="endoutlier" val0="0.001"/>
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31 <flag attr="PVendoutlier"/>
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32 <flag attr="deltaX" val0="12"/>
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33 <flag attr="deltaY" val0="12"/>
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34 <flag attr="xmapchim" val0="12"/>
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35 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
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36 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
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37 <flag attr="hashMultiMatch" val0="30" val1="10"/>
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38 <flag attr="insertThreads" val0="54"/>
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39 <flag attr="nosplit" val0="2"/>
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40 <flag attr="biaswt" val0="0"/>
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41 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
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42 <flag attr="S" val0="-1000"/>
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43 <flag attr="indel"/>
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44 <flag attr="PVres" val0="2"/>
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45 <flag attr="rres" val0="0.9"/>
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46 <flag attr="MaxSE" val0="0.5"/>
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47 <flag attr="HSDrange" val0="1.0"/>
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48 <flag attr="outlierBC"/>
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49 <flag attr="xmapUnique" val0="12"/>
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50 <flag attr="AlignRes" val0="2."/>
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51 <flag attr="outlierExtend" val0="12" val1="24"/>
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52 <flag attr="Kmax" val0="12"/>
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53 <flag attr="resEstimate"/>
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54 <flag attr="f"/>
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55 <flag attr="mres" val0="0.9"/>
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56 </align0>
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57 <align1>
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58 <flag attr="res" val0="2.9"/>
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59 <flag attr="FP" val0="0.6"/>
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60 <flag attr="FN" val0="0.06"/>
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61 <flag attr="sf" val0="0.20"/>
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62 <flag attr="sd" val0="0.0"/>
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63 <flag attr="sr" val0="0.01"/>
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64 <flag attr="extend" val0="1"/>
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65 <flag attr="outlier" val0="0.0001"/>
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66 <flag attr="endoutlier" val0="0.001"/>
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67 <flag attr="PVendoutlier"/>
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68 <flag attr="deltaX" val0="12"/>
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69 <flag attr="deltaY" val0="12"/>
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70 <flag attr="xmapchim" val0="12"/>
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71 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
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72 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
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73 <flag attr="hashMultiMatch" val0="30" val1="10"/>
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74 <flag attr="insertThreads" val0="54"/>
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75 <flag attr="nosplit" val0="2"/>
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76 <flag attr="biaswt" val0="0"/>
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77 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
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78 <flag attr="S" val0="-1000"/>
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79 <flag attr="indel"/>
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80 <flag attr="PVres" val0="2"/>
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81 <flag attr="rres" val0="0.9"/>
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82 <flag attr="MaxSE" val0="0.5"/>
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83 <flag attr="HSDrange" val0="1.0"/>
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84 <flag attr="outlierBC"/>
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85 <flag attr="xmapUnique" val0="12"/>
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86 <flag attr="AlignRes" val0="2."/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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87 <flag attr="outlierExtend" val0="12" val1="24"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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88 <flag attr="Kmax" val0="12"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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89 <flag attr="resEstimate"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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90 <flag attr="f"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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91 <flag attr="mres" val0="0.9"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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92 </align1>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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93 <assignAlignType>
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94 <flag attr="T_cutoff" val0="1e-11" display="P-value" group="Chimeric/conflicting alignment flagging" description="Minimum confidence value used to flag chimeric/conflicting alignments. Recommand to set it to be the same as the merge_Tvalue below."/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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95 <flag attr="max_overhang" val0="5" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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96 </assignAlignType>
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97 <cut_conflicts>
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98 <flag attr="window_size" val0="10000" display="Distance (bp)" group="Conflict-cut" description="The distance (bp) from a conflicting site within which the chimeric quality score of BioNano genome map labels will be examined"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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99 <flag attr="min_quality_score_threshold" val0="35" display="Percent (%)" group="Conflict-cut" description="The minimal percentage of molecules spanning to the left and right of a label of interest, thus supporting the BioNano assembly at that region"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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100 <flag attr="min_coverage_threshold" val0="10" display="Coverage (X)" group="Conflict-cut" description="The minimal number of molecules aligning to a label of interest in the BioNano assembly"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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101 </cut_conflicts>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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102 <mergeNGS_BN>
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103 <flag attr="merge_Tvalue" val0="1e-11" display="P-value" group="Merging" description="Minimum confidence value used to merge alignments. Recommand to set it to be the same as the assignAlignType T_cutoff above"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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104 <flag attr="id_shift" val0="100000" display="BioNano cmap id shift" group="Merging" description="Value to shift the BioNano cmap id to distinguish the BioNano cmaps from sequence cmaps. Recommand to set it to be greater than the number of sequence entries."/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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105 <flag attr="max_merge_rounds" val0="40" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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106 <flag attr="endoutlier" val0="1e-4" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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107 <flag attr="outlier" val0="1e-4" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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108 <flag attr="biaswt" val0="0" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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109 <flag attr="sd" val0="0.1" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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110 <flag attr="res" val0="2.9" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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111 <flag attr="mres" val0="2.9" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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112 <flag attr="sf" val0="0.2" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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113 <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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114 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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115 <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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116 <flag attr="maxmem" val0="960" display=""/>
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117 <flag attr="pairmergeRepeat"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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118 <flag attr="NoBpp"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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119 <flag attr="first" val0="-1" display=""/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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120 <flag attr="f"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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121 </mergeNGS_BN>
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122 <align_final_1st_pass>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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123 <flag attr="res" val0="2.9"/>
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124 <flag attr="FP" val0="0.6"/>
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125 <flag attr="FN" val0="0.06"/>
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126 <flag attr="sf" val0="0.20"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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127 <flag attr="sd" val0="0.0"/>
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128 <flag attr="sr" val0="0.01"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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129 <flag attr="extend" val0="1"/>
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130 <flag attr="outlier" val0="0.0001"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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131 <flag attr="endoutlier" val0="0.001"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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132 <flag attr="PVendoutlier"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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133 <flag attr="deltaX" val0="12"/>
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134 <flag attr="deltaY" val0="12"/>
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135 <flag attr="xmapchim" val0="12"/>
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136 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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137 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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138 <flag attr="hashMultiMatch" val0="30" val1="10"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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139 <flag attr="insertThreads" val0="54"/>
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140 <flag attr="nosplit" val0="2"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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141 <flag attr="biaswt" val0="0"/>
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142 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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143 <flag attr="S" val0="-1000"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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144 <flag attr="indel"/>
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145 <flag attr="PVres" val0="2"/>
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146 <flag attr="rres" val0="0.9"/>
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147 <flag attr="MaxSE" val0="0.5"/>
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148 <flag attr="HSDrange" val0="1.0"/>
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149 <flag attr="outlierBC"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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150 <flag attr="xmapUnique" val0="12"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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151 <flag attr="AlignRes" val0="2."/>
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152 <flag attr="outlierExtend" val0="6" val1="24"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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153 <flag attr="Kmax" val0="6"/>
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154 <flag attr="resEstimate"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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155 <flag attr="f"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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156 <flag attr="mres" val0="0.9"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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157 <flag attr="MultiMatches" val0="5"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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158 </align_final_1st_pass>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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159 <align_final_2nd_pass>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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160 <flag attr="res" val0="2.9"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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161 <flag attr="FP" val0="0.6"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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162 <flag attr="FN" val0="0.06"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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163 <flag attr="sf" val0="0.20"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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164 <flag attr="sd" val0="0.0"/>
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165 <flag attr="sr" val0="0.01"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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166 <flag attr="extend" val0="1"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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167 <flag attr="outlier" val0="0.0001"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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168 <flag attr="endoutlier" val0="0.001"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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169 <flag attr="PVendoutlier"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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170 <flag attr="deltaX" val0="12"/>
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171 <flag attr="deltaY" val0="12"/>
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232 </align_final_BNG>
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258 <flag attr="TB" val0="1e-6" val1="1e-6" val2="-TBmult" val3="0.1"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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259 <flag attr="nosplit" val0="2" display="Allow Chimeric Split" group="Final Refinement" default0="2"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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260 <flag attr="EndTrim" val0="0.0" display="Min End Trim Coverage" group="Final Refinement" default0="4.99"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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261 <flag attr="biaswt" val0="0.7" display="Bias" group="Final Refinement" default0="0"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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262 <flag attr="biaswtEnd" val0="0.0"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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263 <flag attr="biaswtRefine" val0="0.7" val2="1"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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264 <flag attr="biaswtOutlier" val0="0.0"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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265 <flag attr="LRbias" val0="1e0" display="Soft Threshold" group="Final Refinement" default0="1e2"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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266 <flag attr="deltaX" val0="6" display="Molecule Labels Metric" group="Final Refinement" default0="4"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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267 <flag attr="deltaY" val0="7" display="Mapped Labels Metric" group="Final Refinement" default0="6"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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268 <flag attr="RepeatMask" val0="5" val1="0.01" display="Repeat Mask P-values" group="Final Refinement" default0="2" default1="0.01"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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269 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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270 <flag attr="CovTrim" val0="2"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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271 <flag attr="CovTrimLen" val0="55"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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272 <flag attr="TrimNorm" val0="0"/>
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273 <flag attr="TrimNormMed" val0="100"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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274 <flag attr="TrimNormChim" val0="2"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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275 <flag attr="TrimNormMin" val0="2"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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276 <flag attr="PVres" val0="2"/>
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277 <flag attr="PVendoutlier"/>
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278 <flag attr="AlignRes" val0="1.5"/>
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279 <flag attr="rres" val0="1.2"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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280 <flag attr="cres" val0="5.6" val1="3" val2="0.1"/>
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281 <flag attr="hashgen" val00="5" val01="3" val02="2.4" val03="1.5" val04="0.05" val05="5.0" val06="1" val07="1" val08="3"/>
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282 <flag attr="hash" val00="-hashdelta" val01="10" val02="10" val03="-mres" val04="0.9"/>
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283 <flag attr="HSDrange" val0="1.0"/>
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284 <flag attr="hashoffset" val0="1"/>
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285 <flag attr="hashMultiMatch" val0="15"/>
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286 <flag attr="insertThreads" val0="54"/>
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287 <flag attr="BestRef" val0="1"/>
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288 <flag attr="BestRefPV" val0="1"/>
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289 <flag attr="ChimQuality"/>
fec6a0b53189 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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290 <flag attr="f" display="Overwrite Output Files" group="Final Refinement"/>
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291 <flag attr="T" val0="1e-11" display="P Value Cutoff Threshold"/>
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292 </refineFinal1>
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293 </hybridScaffold>