Mercurial > repos > iuc > stacks_clonefilter
comparison macros.xml @ 0:a8a0cd05d47d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
author | iuc |
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date | Sun, 21 May 2017 18:54:11 -0400 |
parents | |
children | 5d12a1115770 |
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-1:000000000000 | 0:a8a0cd05d47d |
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1 <?xml version="1.0"?> | |
2 <macros> | |
3 <xml name="requirements"> | |
4 <requirements> | |
5 <requirement type="package" version="1.46">stacks</requirement> | |
6 <requirement type="package" version="1.2.10">velvet</requirement> | |
7 <requirement type="package" version="1.1">stacks_summary</requirement> | |
8 <yield/> | |
9 </requirements> | |
10 </xml> | |
11 | |
12 <token name="@WRAPPER_VERSION@">1.46</token> | |
13 | |
14 <xml name="stdio"> | |
15 <stdio> | |
16 <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> | |
17 </stdio> | |
18 </xml> | |
19 | |
20 <xml name="citation"> | |
21 <citations> | |
22 <citation type="doi">10.1111/mec.12354</citation> | |
23 <citation type="doi">10.1111/mec.12330</citation> | |
24 <citation type="doi">10.1534/g3.111.000240</citation> | |
25 <citation type="doi">10.1534/genetics.111.127324</citation> | |
26 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> | |
27 <citation type="doi">10.1073/pnas.1006538107</citation> | |
28 </citations> | |
29 </xml> | |
30 | |
31 <token name="@STACKS_INFOS@"> | |
32 <![CDATA[ | |
33 -------- | |
34 | |
35 **Created by:** | |
36 | |
37 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko | |
38 | |
39 **Project links:** | |
40 | |
41 `Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_ | |
42 | |
43 `Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_ | |
44 | |
45 `Stacks google group <http://groups.google.com/group/stacks-users>`_ | |
46 ]]></token> | |
47 | |
48 <xml name="enzymes"> | |
49 <option value="aciI">aciI</option> | |
50 <option value="ageI">ageI</option> | |
51 <option value="aluI">aluI</option> | |
52 <option value="apeKI">apeKI</option> | |
53 <option value="apoI">apoI</option> | |
54 <option value="aseI">aseI</option> | |
55 <option value="bamHI">bamHI</option> | |
56 <option value="bfaI">bfaI</option> | |
57 <option value="bgIII">bgIII</option> | |
58 <option value="bspDI">bspDI</option> | |
59 <option value="bstYI">bstYI</option> | |
60 <option value="claI">claI</option> | |
61 <option value="ddeI">ddeI</option> | |
62 <option value="dpnII">dpnII</option> | |
63 <option value="eaeI">eaeI</option> | |
64 <option value="ecoRI">ecoRI</option> | |
65 <option value="ecoRV">ecoRV</option> | |
66 <option value="ecoT22I">ecoT22I</option> | |
67 <option value="hindIII">hindIII</option> | |
68 <option value="kpnI">kpnI</option> | |
69 <option value="mluCI">mluCI</option> | |
70 <option value="mseI">mseI</option> | |
71 <option value="mspI">mspI</option> | |
72 <option value="ndeI">ndeI</option> | |
73 <option value="nheI">nheI</option> | |
74 <option value="nlaIII">nlaIII</option> | |
75 <option value="notI">notI</option> | |
76 <option value="nsiI">nsiI</option> | |
77 <option value="pstI">pstI</option> | |
78 <option value="rsaI">rsaI</option> | |
79 <option value="sacI">sacI</option> | |
80 <option value="sau3AI">sau3AI</option> | |
81 <option value="sbfI">sbfI</option> | |
82 <option value="sexAI">sexAI</option> | |
83 <option value="sgrAI">sgrAI</option> | |
84 <option value="speI">speI</option> | |
85 <option value="sphI">sphI</option> | |
86 <option value="taqI">taqI</option> | |
87 <option value="xbaI">xbaI</option> | |
88 <option value="xhoI">xhoI</option> | |
89 <option value="csp6I">csp6I</option> | |
90 <option value="bsaHI">bsaHI</option> | |
91 <option value="hpaII">hpaII</option> | |
92 <option value="ncoI">ncoI</option> | |
93 <option value="ApaLI">ApaLI</option> | |
94 </xml> | |
95 | |
96 <xml name="cross_types"> | |
97 <option value="CP">CP (F1 cross)</option> | |
98 <option value="F2">F2 (F2 cross)</option> | |
99 <option value="BC1">BC1 (backcross)</option> | |
100 <option value="DH">DH (double haploid cross)</option> | |
101 <option value="GEN">GEN (generic, unspecific to any map type)</option> | |
102 </xml> | |
103 | |
104 <token name="@CLEAN_EXT@"> | |
105 <![CDATA[ | |
106 #from os.path import splitext | |
107 #import re | |
108 #def clean_ext($identifier) | |
109 #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam')) | |
110 #set $identifier = splitext($identifier)[0] | |
111 #end while | |
112 $identifier#slurp | |
113 #end def | |
114 ]]> | |
115 </token> | |
116 | |
117 <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@"> | |
118 <![CDATA[ | |
119 ## We need to do this as the output file names contains the value of an option (min progeny) | |
120 && | |
121 cd stacks_outputs/ && | |
122 ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv && | |
123 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc && | |
124 ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt && | |
125 ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv && | |
126 cd .. | |
127 ]]> | |
128 </token> | |
129 | |
130 <token name="@NORM_GENOTYPES_OUTPUT_FULL@"> | |
131 <![CDATA[ | |
132 ## We need to do this as the output file names contains the value of an option (min progeny) | |
133 && | |
134 cd stacks_outputs/ && | |
135 ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv && | |
136 ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt && | |
137 ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv && | |
138 ln -s batch_1.genotypes_*.rqtl.tsv batch_1.genotypes.rqtl.tsv && | |
139 ln -s batch_1.haplotypes_*.tsv batch_1.haplotypes.tsv && | |
140 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc && | |
141 ln -s batch_1.genotypes_*.txt batch_1.genotypes.txt && | |
142 ln -s batch_1.genotypes_*[^rqtl].tsv batch_1.genotypes.tsv && | |
143 cd .. | |
144 ]]> | |
145 </token> | |
146 | |
147 <xml name="genotypes_output_light"> | |
148 | |
149 <data format="txt" name="out_joinmap" label="Haplotypes table (JoinMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.loc"> | |
150 <filter>options_usage['rad_analysis_type'] == "genetic"</filter> | |
151 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter> | |
152 </data> | |
153 | |
154 <data format="tabular" name="out_generic_haplo" label="Haplotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"> | |
155 <filter>options_usage['rad_analysis_type'] == "genetic"</filter> | |
156 </data> | |
157 <data format="tabular" name="out_generic_geno" label="Genotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.tsv"> | |
158 <filter>options_usage['rad_analysis_type'] == "genetic"</filter> | |
159 <filter>options_usage['cross_type'] == "GEN"</filter> | |
160 </data> | |
161 | |
162 <data format="tabular" name="out_sql_markers" label="Markers table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"> | |
163 <filter>options_usage['rad_analysis_type'] == "genetic"</filter> | |
164 </data> | |
165 | |
166 <data format="tabular" name="out_sql_genotypes" label="Haplotypes table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.txt"> | |
167 <filter>options_usage['rad_analysis_type'] == "genetic"</filter> | |
168 </data> | |
169 </xml> | |
170 | |
171 <xml name="genotypes_output_full"> | |
172 <!-- Output formats generated by genotypes: | |
173 | |
174 JoinMap, default, only if map type is F2/BC1/DH/CP => batch_1.genotypes_1.loc | |
175 OneMap, only if map type is F2/BC1 => batch_1.genotypes_1onemap.tsv | |
176 OneMap/MapMaker, only if map type is CP => batch_1.genotypes_1.onemap.txt | |
177 Genomic, for all map types => batch_1.genomic_1.tsv | |
178 R/QTL, only if map type is F2/BC1/DH => batch_1.genotypes_1.rqtl.tsv | |
179 | |
180 Additional non-optional output (ie not altered by -o option): | |
181 | |
182 Generic format, for every map types => batch_1.haplotypes_1.tsv | |
183 Generic format, if map type is GEN => batch_1.genotypes_1.tsv --> | |
184 | |
185 <data format="txt" name="out_joinmap" label="Haplotypes table (JoinMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.loc"> | |
186 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter> | |
187 <filter>'map_out' not in options_usage or options_usage['map_out']['map_out_type'] == 'joinmap'</filter> | |
188 </data> | |
189 | |
190 <data format="tabular" name="out_onemap" label="Haplotypes table (OneMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.onemap.txt"> | |
191 <filter>options_usage['cross_type'] in ['F2', 'BC1']</filter> | |
192 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter> | |
193 </data> | |
194 | |
195 <data format="tabular" name="out_onemap_mapmaker" label="Haplotypes table (OneMap/MapMaker format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.onemap.tsv"> | |
196 <filter>options_usage['cross_type'] in ['CP']</filter> | |
197 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter> | |
198 </data> | |
199 | |
200 <data format="tabular" name="out_genomic" label="Haplotypes table (Genomic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genomic.tsv"> | |
201 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'genomic'</filter> | |
202 </data> | |
203 | |
204 <data format="tabular" name="out_rqtl" label="Haplotypes table (R/QTL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.rqtl.tsv"> | |
205 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH']</filter> | |
206 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'rqtl'</filter> | |
207 </data> | |
208 | |
209 <data format="tabular" name="out_generic_haplo" label="Haplotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/> | |
210 | |
211 <data format="tabular" name="out_generic_geno" label="Genotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.tsv"> | |
212 <filter>options_usage['cross_type'] == "GEN"</filter> | |
213 </data> | |
214 | |
215 <data format="tabular" name="out_sql_markers" label="Markers table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"/> | |
216 | |
217 <data format="tabular" name="out_sql_genotypes" label="Haplotypes table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.txt"/> | |
218 </xml> | |
219 | |
220 <xml name="populations_output_light"> | |
221 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"> | |
222 <filter>options_usage['rad_analysis_type'] == "population"</filter> | |
223 </data> | |
224 | |
225 <data format="tabular" name="out_hapstats" label="Haplotype-based summary statistics for each locus in each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hapstats.tsv"> | |
226 <filter>options_usage['rad_analysis_type'] == "population"</filter> | |
227 </data> | |
228 | |
229 <data format="tabular" name="out_populations_log" label="Populations log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.populations.log"> | |
230 <filter>options_usage['rad_analysis_type'] == "population"</filter> | |
231 </data> | |
232 | |
233 <data format="tabular" name="out_sumstats_sum" label="Summary of summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats_summary.tsv"> | |
234 <filter>options_usage['rad_analysis_type'] == "population"</filter> | |
235 </data> | |
236 | |
237 <data format="tabular" name="out_sumstats" label="Summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats.tsv"> | |
238 <filter>options_usage['rad_analysis_type'] == "population"</filter> | |
239 </data> | |
240 | |
241 <data format="tabular" name="out_sql" label="Stacks SQL format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"> | |
242 <filter>options_usage['rad_analysis_type'] == "population"</filter> | |
243 </data> | |
244 </xml> | |
245 | |
246 <xml name="populations_output_full"> | |
247 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/> | |
248 | |
249 <data format="tabular" name="out_hapstats" label="Haplotype-based summary statistics for each locus in each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hapstats.tsv"/> | |
250 | |
251 <data format="tabular" name="out_populations_log" label="Populations log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.populations.log"/> | |
252 | |
253 <data format="tabular" name="out_sumstats_sum" label="Summary of summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats_summary.tsv"/> | |
254 | |
255 <data format="tabular" name="out_sumstats" label="Summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats.tsv"/> | |
256 | |
257 <data format="tabular" name="out_sql" label="Stacks SQL format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"/> | |
258 | |
259 <data format="tabular" name="out_fstats" label="SNP and Haplotype-based F statistics with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phistats.tsv"> | |
260 <filter>fstats</filter> | |
261 </data> | |
262 <data format="tabular" name="out_fasta" label="Full sequence for each unique haplotype (regardless of plausibility) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fa"> | |
263 <filter>populations_output['fasta']</filter> | |
264 </data> | |
265 <data format="tabular" name="out_phylip_all_partitions" label="Phylip all (partitions) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fullseq.partitions.phylip"> | |
266 <filter>populations_output['phylip_var_all']</filter> | |
267 </data> | |
268 <data format="tabular" name="out_phylip_all_pop" label="Phylip all (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fullseq.phylip"> | |
269 <filter>populations_output['phylip_var_all']</filter> | |
270 </data> | |
271 <data format="tabular" name="out_phylip_all_loci" label="Phylip all (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1fullseq.phylip.log"> | |
272 <filter>populations_output['phylip_var_all']</filter> | |
273 </data> | |
274 <data format="tabular" name="out_genepop" label="GenePop formatwith ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genepop"> | |
275 <filter>populations_output['genepop']</filter> | |
276 </data> | |
277 <data format="tabular" name="out_vcf_haplotypes" label="Haplotypes in VCF format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.vcf"> | |
278 <filter>populations_output['vcf_haplotypes']</filter> | |
279 </data> | |
280 <data format="tabular" name="out_hzar" label="Genotypes in Hybrid Zone Analysis using R (HAZR) format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hzar.csv"> | |
281 <filter>populations_output['hzar']</filter> | |
282 </data> | |
283 <data format="tabular" name="out_beagle_phased_haplotypes" label="Beagle format (phased, haplotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.phased.bgl"> | |
284 <filter>populations_output['beagle_phased']</filter> | |
285 </data> | |
286 <data format="tabular" name="out_beagle_phased_markers" label="Beagle format (phased, markers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.phased.bgl.markers"> | |
287 <filter>populations_output['beagle_phased']</filter> | |
288 </data> | |
289 <data format="tabular" name="out_beagle_haplotypes" label="Beagle format (haplotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.unphased.bgl"> | |
290 <filter>populations_output['beagle']</filter> | |
291 </data> | |
292 <data format="tabular" name="out_beagle_markers" label="Beagle format (markers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.unphased.bgl.markers"> | |
293 <filter>populations_output['beagle']</filter> | |
294 </data> | |
295 <data format="tabular" name="out_phylip_pop" label="Phylip (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip"> | |
296 <filter>populations_output['phylip']</filter> | |
297 </data> | |
298 <data format="tabular" name="out_phylip_loci" label="Phylip (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip.log"> | |
299 <filter>populations_output['phylip']</filter> | |
300 </data> | |
301 <data format="tabular" name="out_plink_markers" label="PLINK (makers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.plink.map"> | |
302 <filter>populations_output['plink']</filter> | |
303 </data> | |
304 <data format="tabular" name="out_plink_genotypes" label="PLINK format (genotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.plink.ped"> | |
305 <filter>populations_output['plink']</filter> | |
306 </data> | |
307 <data format="tabular" name="out_fasta_strict" label="Full sequence for each haplotype (only for biologically plausible loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.strict.fa"> | |
308 <filter>populations_output['fasta_strict']</filter> | |
309 </data> | |
310 <data format="tabular" name="out_structure" label="Structure format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.structure.tsv"> | |
311 <filter>populations_output['structure']</filter> | |
312 </data> | |
313 <data format="tabular" name="out_treemix_pop" label="TreeMix format (population) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.treemix"> | |
314 <filter>populations_output['treemix']</filter> | |
315 </data> | |
316 <data format="tabular" name="out_treemix_loci" label="TreeMix format (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.treemix.log"> | |
317 <filter>populations_output['treemix']</filter> | |
318 </data> | |
319 <data format="tabular" name="out_fastpĥase" label="fastPHASE format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.un.fastphase.inp"> | |
320 <filter>populations_output['fastphase']</filter> | |
321 </data> | |
322 <data format="tabular" name="out_phase" label="PHASE format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.un.phase.inp"> | |
323 <filter>populations_output['phase']</filter> | |
324 </data> | |
325 <data format="tabular" name="out_vcf" label="SNPs in VCF format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.vcf"> | |
326 <filter>populations_output['vcf']</filter> | |
327 </data> | |
328 <data format="tabular" name="out_genomic" label="Each nucleotide position in all population members with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genomic.tsv"> | |
329 <filter>populations_output['options_genomic']['genomic']</filter> | |
330 </data> | |
331 | |
332 </xml> | |
333 | |
334 <xml name="snp_options"> | |
335 <conditional name="select_model"> | |
336 <param name="model_type" type="select" label="Choose the model"> | |
337 <option value="snp" selected="true">SNP</option> | |
338 <option value="bounded">Bounded SNP</option> | |
339 <option value="fixed">Fixed</option> | |
340 </param> | |
341 <when value="snp"> | |
342 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > | |
343 <option value="0.1">0.1</option> | |
344 <option value="0.05" selected="True">0.05</option> | |
345 <option value="0.01">0.01</option> | |
346 <option value="0.001">0.001</option> | |
347 </param> | |
348 </when> | |
349 <when value="bounded"> | |
350 <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> | |
351 <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> | |
352 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > | |
353 <option value="0.1">0.1</option> | |
354 <option value="0.05" selected="True">0.05</option> | |
355 <option value="0.01">0.01</option> | |
356 <option value="0.001">0.001</option> | |
357 </param> | |
358 </when> | |
359 <when value="fixed"> | |
360 </when> | |
361 </conditional> | |
362 </xml> | |
363 | |
364 <xml name="snp_options_full"> | |
365 <conditional name="select_model"> | |
366 <param name="model_type" type="select" label="Choose the model"> | |
367 <option value="snp" selected="true">SNP</option> | |
368 <option value="bounded">Bounded SNP</option> | |
369 <option value="fixed">Fixed</option> | |
370 </param> | |
371 <when value="snp"> | |
372 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > | |
373 <option value="0.1">0.1</option> | |
374 <option value="0.05" selected="True">0.05</option> | |
375 <option value="0.01">0.01</option> | |
376 <option value="0.001">0.001</option> | |
377 </param> | |
378 </when> | |
379 <when value="bounded"> | |
380 <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> | |
381 <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> | |
382 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > | |
383 <option value="0.1">0.1</option> | |
384 <option value="0.05" selected="True">0.05</option> | |
385 <option value="0.01">0.01</option> | |
386 <option value="0.001">0.001</option> | |
387 </param> | |
388 </when> | |
389 <when value="fixed"> | |
390 <param name="bc_err_freq" argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> | |
391 </when> | |
392 </conditional> | |
393 </xml> | |
394 | |
395 <xml name="barcode_encoding_single"> | |
396 <option value="--inline_null" selected="True">Barcode is inline with sequence</option> | |
397 <option value="--index_null">Barcode is provided in FASTQ header</option> | |
398 </xml> | |
399 | |
400 <xml name="barcode_encoding_pair"> | |
401 <option value="--inline_null" selected="True">Barcode is inline with sequence</option> | |
402 <option value="--null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> | |
403 <option value="--index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> | |
404 <option value="--inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> | |
405 <option value="--index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> | |
406 <option value="--inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> | |
407 <option value="--index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option> | |
408 </xml> | |
409 </macros> |