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comparison 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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1 <hybridScaffold>
2 <version>
3 <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/>
4 </version>
5 <global>
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."/>
7 <flag attr="maxthreads" val0="54" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
8 <flag attr="maxvirtmem" val0="960"/>
9 <flag attr="RAmem" val0="3" val1="1"/>
10 </global>
11 <fasta2cmap>
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."/>
13 <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
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."/>
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."/>
16 </fasta2cmap>
17 <align0>
18 <flag attr="M" val0="1" val1="3"/>
19 <flag attr="ScaleDelta" val0="0.02" val1="15"/>
20 <flag attr="ScaleDeltaBPP"/>
21 <flag attr="hashScaleDelta" val0="2"/>
22 <flag attr="res" val0="2.9"/>
23 <flag attr="FP" val0="0.6"/>
24 <flag attr="FN" val0="0.06"/>
25 <flag attr="sf" val0="0.20"/>
26 <flag attr="sd" val0="0.0"/>
27 <flag attr="sr" val0="0.01"/>
28 <flag attr="extend" val0="1"/>
29 <flag attr="outlier" val0="0.0001"/>
30 <flag attr="endoutlier" val0="0.001"/>
31 <flag attr="PVendoutlier"/>
32 <flag attr="deltaX" val0="12"/>
33 <flag attr="deltaY" val0="12"/>
34 <flag attr="xmapchim" val0="12"/>
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"/>
36 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
37 <flag attr="hashMultiMatch" val0="30" val1="10"/>
38 <flag attr="insertThreads" val0="54"/>
39 <flag attr="nosplit" val0="2"/>
40 <flag attr="biaswt" val0="0"/>
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."/>
42 <flag attr="S" val0="-1000"/>
43 <flag attr="indel"/>
44 <flag attr="PVres" val0="2"/>
45 <flag attr="rres" val0="0.9"/>
46 <flag attr="MaxSE" val0="0.5"/>
47 <flag attr="HSDrange" val0="1.0"/>
48 <flag attr="outlierBC"/>
49 <flag attr="xmapUnique" val0="12"/>
50 <flag attr="AlignRes" val0="2."/>
51 <flag attr="outlierExtend" val0="12" val1="24"/>
52 <flag attr="Kmax" val0="12"/>
53 <flag attr="resEstimate"/>
54 <flag attr="f"/>
55 <flag attr="mres" val0="0.9"/>
56 </align0>
57 <align1>
58 <flag attr="res" val0="2.9"/>
59 <flag attr="FP" val0="0.6"/>
60 <flag attr="FN" val0="0.06"/>
61 <flag attr="sf" val0="0.20"/>
62 <flag attr="sd" val0="0.0"/>
63 <flag attr="sr" val0="0.01"/>
64 <flag attr="extend" val0="1"/>
65 <flag attr="outlier" val0="0.0001"/>
66 <flag attr="endoutlier" val0="0.001"/>
67 <flag attr="PVendoutlier"/>
68 <flag attr="deltaX" val0="12"/>
69 <flag attr="deltaY" val0="12"/>
70 <flag attr="xmapchim" val0="12"/>
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"/>
72 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
73 <flag attr="hashMultiMatch" val0="30" val1="10"/>
74 <flag attr="insertThreads" val0="54"/>
75 <flag attr="nosplit" val0="2"/>
76 <flag attr="biaswt" val0="0"/>
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."/>
78 <flag attr="S" val0="-1000"/>
79 <flag attr="indel"/>
80 <flag attr="PVres" val0="2"/>
81 <flag attr="rres" val0="0.9"/>
82 <flag attr="MaxSE" val0="0.5"/>
83 <flag attr="HSDrange" val0="1.0"/>
84 <flag attr="outlierBC"/>
85 <flag attr="xmapUnique" val0="12"/>
86 <flag attr="AlignRes" val0="2."/>
87 <flag attr="outlierExtend" val0="12" val1="24"/>
88 <flag attr="Kmax" val0="12"/>
89 <flag attr="resEstimate"/>
90 <flag attr="f"/>
91 <flag attr="mres" val0="0.9"/>
92 </align1>
93 <assignAlignType>
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."/>
95 <flag attr="max_overhang" val0="5" display=""/>
96 </assignAlignType>
97 <cut_conflicts>
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"/>
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"/>
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"/>
101 </cut_conflicts>
102 <mergeNGS_BN>
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"/>
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."/>
105 <flag attr="max_merge_rounds" val0="40" display=""/>
106 <flag attr="endoutlier" val0="1e-4" display=""/>
107 <flag attr="outlier" val0="1e-4" display=""/>
108 <flag attr="biaswt" val0="0" display=""/>
109 <flag attr="sd" val0="0.1" display=""/>
110 <flag attr="res" val0="2.9" display=""/>
111 <flag attr="mres" val0="2.9" display=""/>
112 <flag attr="sf" val0="0.2" display=""/>
113 <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
114 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
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."/>
116 <flag attr="maxmem" val0="960" display=""/>
117 <flag attr="pairmergeRepeat"/>
118 <flag attr="NoBpp"/>
119 <flag attr="first" val0="-1" display=""/>
120 <flag attr="f"/>
121 </mergeNGS_BN>
122 <align_final_1st_pass>
123 <flag attr="res" val0="2.9"/>
124 <flag attr="FP" val0="0.6"/>
125 <flag attr="FN" val0="0.06"/>
126 <flag attr="sf" val0="0.20"/>
127 <flag attr="sd" val0="0.0"/>
128 <flag attr="sr" val0="0.01"/>
129 <flag attr="extend" val0="1"/>
130 <flag attr="outlier" val0="0.0001"/>
131 <flag attr="endoutlier" val0="0.001"/>
132 <flag attr="PVendoutlier"/>
133 <flag attr="deltaX" val0="12"/>
134 <flag attr="deltaY" val0="12"/>
135 <flag attr="xmapchim" val0="12"/>
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"/>
137 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
138 <flag attr="hashMultiMatch" val0="30" val1="10"/>
139 <flag attr="insertThreads" val0="54"/>
140 <flag attr="nosplit" val0="2"/>
141 <flag attr="biaswt" val0="0"/>
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."/>
143 <flag attr="S" val0="-1000"/>
144 <flag attr="indel"/>
145 <flag attr="PVres" val0="2"/>
146 <flag attr="rres" val0="0.9"/>
147 <flag attr="MaxSE" val0="0.5"/>
148 <flag attr="HSDrange" val0="1.0"/>
149 <flag attr="outlierBC"/>
150 <flag attr="xmapUnique" val0="12"/>
151 <flag attr="AlignRes" val0="2."/>
152 <flag attr="outlierExtend" val0="6" val1="24"/>
153 <flag attr="Kmax" val0="6"/>
154 <flag attr="resEstimate"/>
155 <flag attr="f"/>
156 <flag attr="mres" val0="0.9"/>
157 <flag attr="MultiMatches" val0="5"/>
158 </align_final_1st_pass>
159 <align_final_2nd_pass>
160 <flag attr="res" val0="2.9"/>
161 <flag attr="FP" val0="0.6"/>
162 <flag attr="FN" val0="0.06"/>
163 <flag attr="sf" val0="0.20"/>
164 <flag attr="sd" val0="0.0"/>
165 <flag attr="sr" val0="0.01"/>
166 <flag attr="extend" val0="1"/>
167 <flag attr="outlier" val0="0.0001"/>
168 <flag attr="endoutlier" val0="0.001"/>
169 <flag attr="PVendoutlier"/>
170 <flag attr="deltaX" val0="12"/>
171 <flag attr="deltaY" val0="12"/>
172 <flag attr="xmapchim" val0="12"/>
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"/>
174 <flag attr="hash" val0="-hashdelta" val1="50"/>
175 <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/>
176 <flag attr="insertThreads" val0="54"/>
177 <flag attr="nosplit" val0="2"/>
178 <flag attr="biaswt" val0="0"/>
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."/>
180 <flag attr="S" val0="-1000"/>
181 <flag attr="indel"/>
182 <flag attr="PVres" val0="2"/>
183 <flag attr="rres" val0="0.9"/>
184 <flag attr="MaxSE" val0="0.5"/>
185 <flag attr="HSDrange" val0="1.0"/>
186 <flag attr="outlierBC"/>
187 <flag attr="xmapUnique" val0="12"/>
188 <flag attr="AlignRes" val0="2."/>
189 <flag attr="outlierExtend" val0="12" val1="24"/>
190 <flag attr="Kmax" val0="12"/>
191 <flag attr="resEstimate"/>
192 <flag attr="f"/>
193 <flag attr="mres" val0="0.9"/>
194 <flag attr="MultiMatches" val0="5"/>
195 </align_final_2nd_pass>
196 <align_final_BNG>
197 <flag attr="res" val0="2.9"/>
198 <flag attr="FP" val0="0.6"/>
199 <flag attr="FN" val0="0.06"/>
200 <flag attr="sf" val0="0.20"/>
201 <flag attr="sd" val0="0.0"/>
202 <flag attr="sr" val0="0.01"/>
203 <flag attr="extend" val0="1"/>
204 <flag attr="outlier" val0="0.0001"/>
205 <flag attr="endoutlier" val0="0.001"/>
206 <flag attr="PVendoutlier"/>
207 <flag attr="deltaX" val0="6"/>
208 <flag attr="deltaY" val0="6"/>
209 <flag attr="xmapchim" val0="12"/>
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"/>
211 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
212 <flag attr="hashMultiMatch" val0="30" val1="10"/>
213 <flag attr="insertThreads" val0="4"/>
214 <flag attr="nosplit" val0="2"/>
215 <flag attr="biaswt" val0="0"/>
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."/>
217 <flag attr="S" val0="-1000"/>
218 <flag attr="indel"/>
219 <flag attr="PVres" val0="2"/>
220 <flag attr="rres" val0="0.9"/>
221 <flag attr="MaxSE" val0="0.5"/>
222 <flag attr="HSDrange" val0="1.0"/>
223 <flag attr="outlierBC"/>
224 <flag attr="xmapUnique" val0="14"/>
225 <flag attr="AlignRes" val0="2."/>
226 <flag attr="outlierExtend" val0="6" val1="24"/>
227 <flag attr="Kmax" val0="6"/>
228 <flag attr="resEstimate"/>
229 <flag attr="BestRef" val0="1"/>
230 <flag attr="f"/>
231 <flag attr="mres" val0="0.9"/>
232 </align_final_BNG>
233 <refineFinal1>
234 <flag attr="refine" val0="1" display="Refine Map" group="Final Refinement" default0="3"/>
235 <flag attr="usecolor" val0="1" default0="1" display="Color Channel" group="Final Refinement"/>
236 <flag attr="A" val0="5" display="Aligned Sites Threshold" group="Final Refinement" default0="5"/>
237 <flat attr="S" val0="-9"/>
238 <flag attr="L" val0="130"/>
239 <flag attr="maptype" val0="0"/>
240 <flag attr="extend" val0="1" display="Allow Extended Molecule" group="Final Refinement" default0="1"/>
241 <flag attr="MaxCov" val0="100" display="Max Coverage" group="Final Refinement" default0="100"/>
242 <flag attr="Mprobeval" display="Fast Mode" group="Final Refinement"/>
243 <flag attr="splitcnt"/>
244 <flag attr="splitrev" val0="2"/>
245 <flag attr="CmapSNR"/>
246 <flag attr="splitsite"/>
247 <flag attr="MinSplitLen" val0="50.0"/>
248 <flag attr="MaxSE" val0="0.5"/>
249 <flag attr="outlier" val0="2e-2" display="Min Outliers P-value" group="Second Refinement" default0="1e-5"/>
250 <flag attr="outlierMax" val0="80."/>
251 <flag attr="outlierLambda" val0="20."/>
252 <flag attr="endoutlier" val0="1e-3" display="Molecule Ends P-value Cutoff" group="Second Refinement" default0="1e-4"/>
253 <flag attr="endoutlierRef" val0="1e-4" val1="1e-3"/>
254 <flag attr="skip_dist" val0="0.0" val2="0.0"/>
255 <flag attr="endoutlierFinal" val0="1"/>
256 <flag attr="maxEnd" val0="90."/>
257 <flag attr="RTHETA_FIX" val0="0"/>
258 <flag attr="TB" val0="1e-6" val1="1e-6" val2="-TBmult" val3="0.1"/>
259 <flag attr="nosplit" val0="2" display="Allow Chimeric Split" group="Final Refinement" default0="2"/>
260 <flag attr="EndTrim" val0="0.0" display="Min End Trim Coverage" group="Final Refinement" default0="4.99"/>
261 <flag attr="biaswt" val0="0.7" display="Bias" group="Final Refinement" default0="0"/>
262 <flag attr="biaswtEnd" val0="0.0"/>
263 <flag attr="biaswtRefine" val0="0.7" val2="1"/>
264 <flag attr="biaswtOutlier" val0="0.0"/>
265 <flag attr="LRbias" val0="1e0" display="Soft Threshold" group="Final Refinement" default0="1e2"/>
266 <flag attr="deltaX" val0="6" display="Molecule Labels Metric" group="Final Refinement" default0="4"/>
267 <flag attr="deltaY" val0="7" display="Mapped Labels Metric" group="Final Refinement" default0="6"/>
268 <flag attr="RepeatMask" val0="5" val1="0.01" display="Repeat Mask P-values" group="Final Refinement" default0="2" default1="0.01"/>
269 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4"/>
270 <flag attr="CovTrim" val0="2"/>
271 <flag attr="CovTrimLen" val0="55"/>
272 <flag attr="TrimNorm" val0="0"/>
273 <flag attr="TrimNormMed" val0="100"/>
274 <flag attr="TrimNormChim" val0="2"/>
275 <flag attr="TrimNormMin" val0="2"/>
276 <flag attr="PVres" val0="2"/>
277 <flag attr="PVendoutlier"/>
278 <flag attr="AlignRes" val0="1.5"/>
279 <flag attr="rres" val0="1.2"/>
280 <flag attr="cres" val0="5.6" val1="3" val2="0.1"/>
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"/>
282 <flag attr="hash" val00="-hashdelta" val01="10" val02="10" val03="-mres" val04="0.9"/>
283 <flag attr="HSDrange" val0="1.0"/>
284 <flag attr="hashoffset" val0="1"/>
285 <flag attr="hashMultiMatch" val0="15"/>
286 <flag attr="insertThreads" val0="54"/>
287 <flag attr="BestRef" val0="1"/>
288 <flag attr="BestRefPV" val0="1"/>
289 <flag attr="ChimQuality"/>
290 <flag attr="f" display="Overwrite Output Files" group="Final Refinement"/>
291 <flag attr="T" val0="1e-11" display="P Value Cutoff Threshold"/>
292 </refineFinal1>
293 </hybridScaffold>