Mercurial > repos > bgruening > bionano_scaffold
annotate test-data/configuration.xml @ 10:22286dab5aa1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
author | bgruening |
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date | Wed, 18 Jan 2023 15:22:13 +0000 |
parents | fec6a0b53189 |
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fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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1 <hybridScaffold> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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2 <version> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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3 <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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4 </version> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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5 <global> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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8 <flag attr="maxvirtmem" val0="960"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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9 <flag attr="RAmem" val0="3" val1="1"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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10 </global> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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11 <fasta2cmap> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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16 </fasta2cmap> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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17 <align0> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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18 <flag attr="M" val0="1" val1="3"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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19 <flag attr="ScaleDelta" val0="0.02" val1="15"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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20 <flag attr="ScaleDeltaBPP"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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21 <flag attr="hashScaleDelta" val0="2"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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22 <flag attr="res" val0="2.9"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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23 <flag attr="FP" val0="0.6"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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24 <flag attr="FN" val0="0.06"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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25 <flag attr="sf" val0="0.20"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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26 <flag attr="sd" val0="0.0"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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27 <flag attr="sr" val0="0.01"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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28 <flag attr="extend" val0="1"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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29 <flag attr="outlier" val0="0.0001"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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30 <flag attr="endoutlier" val0="0.001"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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31 <flag attr="PVendoutlier"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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32 <flag attr="deltaX" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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33 <flag attr="deltaY" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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34 <flag attr="xmapchim" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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"/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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36 <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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37 <flag attr="hashMultiMatch" val0="30" val1="10"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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38 <flag attr="insertThreads" val0="54"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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39 <flag attr="nosplit" val0="2"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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40 <flag attr="biaswt" val0="0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
fec6a0b53189
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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42 <flag attr="S" val0="-1000"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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43 <flag attr="indel"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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44 <flag attr="PVres" val0="2"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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45 <flag attr="rres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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46 <flag attr="MaxSE" val0="0.5"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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47 <flag attr="HSDrange" val0="1.0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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48 <flag attr="outlierBC"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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49 <flag attr="xmapUnique" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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50 <flag attr="AlignRes" val0="2."/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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51 <flag attr="outlierExtend" val0="12" val1="24"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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52 <flag attr="Kmax" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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53 <flag attr="resEstimate"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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54 <flag attr="f"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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55 <flag attr="mres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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56 </align0> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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57 <align1> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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58 <flag attr="res" val0="2.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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59 <flag attr="FP" val0="0.6"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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60 <flag attr="FN" val0="0.06"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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61 <flag attr="sf" val0="0.20"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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62 <flag attr="sd" val0="0.0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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63 <flag attr="sr" val0="0.01"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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64 <flag attr="extend" val0="1"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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65 <flag attr="outlier" val0="0.0001"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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66 <flag attr="endoutlier" val0="0.001"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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67 <flag attr="PVendoutlier"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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68 <flag attr="deltaX" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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69 <flag attr="deltaY" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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70 <flag attr="xmapchim" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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72 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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75 <flag attr="nosplit" val0="2"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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76 <flag attr="biaswt" val0="0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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78 <flag attr="S" val0="-1000"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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79 <flag attr="indel"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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80 <flag attr="PVres" val0="2"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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81 <flag attr="rres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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82 <flag attr="MaxSE" val0="0.5"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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83 <flag attr="HSDrange" val0="1.0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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84 <flag attr="outlierBC"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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85 <flag attr="xmapUnique" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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86 <flag attr="AlignRes" val0="2."/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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87 <flag attr="outlierExtend" val0="12" val1="24"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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88 <flag attr="Kmax" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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89 <flag attr="resEstimate"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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90 <flag attr="f"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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91 <flag attr="mres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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92 </align1> |
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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=""/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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"/> |
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"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"/> |
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"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"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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101 </cut_conflicts> |
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102 <mergeNGS_BN> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
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"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=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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106 <flag attr="endoutlier" val0="1e-4" display=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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107 <flag attr="outlier" val0="1e-4" display=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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108 <flag attr="biaswt" val0="0" display=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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109 <flag attr="sd" val0="0.1" display=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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110 <flag attr="res" val0="2.9" display=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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111 <flag attr="mres" val0="2.9" display=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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112 <flag attr="sf" val0="0.2" display=""/> |
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"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=""/> |
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"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=""/> |
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"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."/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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117 <flag attr="pairmergeRepeat"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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118 <flag attr="NoBpp"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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119 <flag attr="first" val0="-1" display=""/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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120 <flag attr="f"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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121 </mergeNGS_BN> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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122 <align_final_1st_pass> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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124 <flag attr="FP" val0="0.6"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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125 <flag attr="FN" val0="0.06"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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126 <flag attr="sf" val0="0.20"/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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128 <flag attr="sr" val0="0.01"/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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130 <flag attr="outlier" val0="0.0001"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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131 <flag attr="endoutlier" val0="0.001"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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132 <flag attr="PVendoutlier"/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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134 <flag attr="deltaY" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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135 <flag attr="xmapchim" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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"/> |
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"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"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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138 <flag attr="hashMultiMatch" val0="30" val1="10"/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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140 <flag attr="nosplit" val0="2"/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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."/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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143 <flag attr="S" val0="-1000"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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144 <flag attr="indel"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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145 <flag attr="PVres" val0="2"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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146 <flag attr="rres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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147 <flag attr="MaxSE" val0="0.5"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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148 <flag attr="HSDrange" val0="1.0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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149 <flag attr="outlierBC"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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150 <flag attr="xmapUnique" val0="12"/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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152 <flag attr="outlierExtend" val0="6" val1="24"/> |
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"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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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154 <flag attr="resEstimate"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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155 <flag attr="f"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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156 <flag attr="mres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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157 <flag attr="MultiMatches" val0="5"/> |
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158 </align_final_1st_pass> |
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159 <align_final_2nd_pass> |
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160 <flag attr="res" val0="2.9"/> |
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161 <flag attr="FP" val0="0.6"/> |
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162 <flag attr="FN" val0="0.06"/> |
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163 <flag attr="sf" val0="0.20"/> |
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164 <flag attr="sd" val0="0.0"/> |
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165 <flag attr="sr" val0="0.01"/> |
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166 <flag attr="extend" val0="1"/> |
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167 <flag attr="outlier" val0="0.0001"/> |
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168 <flag attr="endoutlier" val0="0.001"/> |
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169 <flag attr="PVendoutlier"/> |
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170 <flag attr="deltaX" val0="12"/> |
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171 <flag attr="deltaY" val0="12"/> |
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172 <flag attr="xmapchim" val0="12"/> |
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173 <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> |
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174 <flag attr="hash" val0="-hashdelta" val1="50"/> |
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175 <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/> |
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176 <flag attr="insertThreads" val0="54"/> |
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177 <flag attr="nosplit" val0="2"/> |
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178 <flag attr="biaswt" val0="0"/> |
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179 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/> |
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180 <flag attr="S" val0="-1000"/> |
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181 <flag attr="indel"/> |
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182 <flag attr="PVres" val0="2"/> |
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183 <flag attr="rres" val0="0.9"/> |
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184 <flag attr="MaxSE" val0="0.5"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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185 <flag attr="HSDrange" val0="1.0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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186 <flag attr="outlierBC"/> |
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187 <flag attr="xmapUnique" val0="12"/> |
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188 <flag attr="AlignRes" val0="2."/> |
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189 <flag attr="outlierExtend" val0="12" val1="24"/> |
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190 <flag attr="Kmax" val0="12"/> |
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191 <flag attr="resEstimate"/> |
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192 <flag attr="f"/> |
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193 <flag attr="mres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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194 <flag attr="MultiMatches" val0="5"/> |
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195 </align_final_2nd_pass> |
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196 <align_final_BNG> |
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197 <flag attr="res" val0="2.9"/> |
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198 <flag attr="FP" val0="0.6"/> |
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199 <flag attr="FN" val0="0.06"/> |
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200 <flag attr="sf" val0="0.20"/> |
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201 <flag attr="sd" val0="0.0"/> |
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202 <flag attr="sr" val0="0.01"/> |
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203 <flag attr="extend" val0="1"/> |
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204 <flag attr="outlier" val0="0.0001"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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205 <flag attr="endoutlier" val0="0.001"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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206 <flag attr="PVendoutlier"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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207 <flag attr="deltaX" val0="6"/> |
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208 <flag attr="deltaY" val0="6"/> |
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209 <flag attr="xmapchim" val0="12"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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210 <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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211 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> |
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212 <flag attr="hashMultiMatch" val0="30" val1="10"/> |
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213 <flag attr="insertThreads" val0="4"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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214 <flag attr="nosplit" val0="2"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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215 <flag attr="biaswt" val0="0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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216 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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217 <flag attr="S" val0="-1000"/> |
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218 <flag attr="indel"/> |
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219 <flag attr="PVres" val0="2"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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220 <flag attr="rres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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221 <flag attr="MaxSE" val0="0.5"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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222 <flag attr="HSDrange" val0="1.0"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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223 <flag attr="outlierBC"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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224 <flag attr="xmapUnique" val0="14"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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225 <flag attr="AlignRes" val0="2."/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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226 <flag attr="outlierExtend" val0="6" val1="24"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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227 <flag attr="Kmax" val0="6"/> |
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228 <flag attr="resEstimate"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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229 <flag attr="BestRef" val0="1"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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230 <flag attr="f"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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231 <flag attr="mres" val0="0.9"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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232 </align_final_BNG> |
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233 <refineFinal1> |
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234 <flag attr="refine" val0="1" display="Refine Map" group="Final Refinement" default0="3"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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235 <flag attr="usecolor" val0="1" default0="1" display="Color Channel" group="Final Refinement"/> |
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236 <flag attr="A" val0="5" display="Aligned Sites Threshold" group="Final Refinement" default0="5"/> |
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237 <flat attr="S" val0="-9"/> |
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238 <flag attr="L" val0="130"/> |
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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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239 <flag attr="maptype" val0="0"/> |
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240 <flag attr="extend" val0="1" display="Allow Extended Molecule" group="Final Refinement" default0="1"/> |
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241 <flag attr="MaxCov" val0="100" display="Max Coverage" group="Final Refinement" default0="100"/> |
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242 <flag attr="Mprobeval" display="Fast Mode" group="Final Refinement"/> |
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243 <flag attr="splitcnt"/> |
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244 <flag attr="splitrev" val0="2"/> |
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245 <flag attr="CmapSNR"/> |
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246 <flag attr="splitsite"/> |
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247 <flag attr="MinSplitLen" val0="50.0"/> |
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248 <flag attr="MaxSE" val0="0.5"/> |
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249 <flag attr="outlier" val0="2e-2" display="Min Outliers P-value" group="Second Refinement" default0="1e-5"/> |
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250 <flag attr="outlierMax" val0="80."/> |
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251 <flag attr="outlierLambda" val0="20."/> |
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252 <flag attr="endoutlier" val0="1e-3" display="Molecule Ends P-value Cutoff" group="Second Refinement" default0="1e-4"/> |
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253 <flag attr="endoutlierRef" val0="1e-4" val1="1e-3"/> |
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254 <flag attr="skip_dist" val0="0.0" val2="0.0"/> |
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255 <flag attr="endoutlierFinal" val0="1"/> |
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256 <flag attr="maxEnd" val0="90."/> |
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257 <flag attr="RTHETA_FIX" val0="0"/> |
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258 <flag attr="TB" val0="1e-6" val1="1e-6" val2="-TBmult" val3="0.1"/> |
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259 <flag attr="nosplit" val0="2" display="Allow Chimeric Split" group="Final Refinement" default0="2"/> |
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260 <flag attr="EndTrim" val0="0.0" display="Min End Trim Coverage" group="Final Refinement" default0="4.99"/> |
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261 <flag attr="biaswt" val0="0.7" display="Bias" group="Final Refinement" default0="0"/> |
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262 <flag attr="biaswtEnd" val0="0.0"/> |
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263 <flag attr="biaswtRefine" val0="0.7" val2="1"/> |
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264 <flag attr="biaswtOutlier" val0="0.0"/> |
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265 <flag attr="LRbias" val0="1e0" display="Soft Threshold" group="Final Refinement" default0="1e2"/> |
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266 <flag attr="deltaX" val0="6" display="Molecule Labels Metric" group="Final Refinement" default0="4"/> |
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267 <flag attr="deltaY" val0="7" display="Mapped Labels Metric" group="Final Refinement" default0="6"/> |
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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"/> |
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269 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4"/> |
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270 <flag attr="CovTrim" val0="2"/> |
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271 <flag attr="CovTrimLen" val0="55"/> |
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272 <flag attr="TrimNorm" val0="0"/> |
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273 <flag attr="TrimNormMed" val0="100"/> |
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274 <flag attr="TrimNormChim" val0="2"/> |
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275 <flag attr="TrimNormMin" val0="2"/> |
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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"/> |
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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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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be"
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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"/> |
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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> |