Mercurial > repos > iuc > stacks_clonefilter

comparison macros.xml @ 0:a8a0cd05d47d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
author iuc
date Sun, 21 May 2017 18:54:11 -0400
parents
children 5d12a1115770
comparison
equal deleted inserted replaced
-1:000000000000 0:a8a0cd05d47d
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>