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comparison macros.xml @ 0:66d3c1ae3937 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
author iuc
date Tue, 14 Jun 2016 14:06:44 -0400
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children 26ad8a52d9fd
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-1:000000000000 0:66d3c1ae3937
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="1.40">stacks</requirement>
6 <requirement type="package" version="1.2.10">velvet</requirement>
7 <container type="docker">quay.io/mulled/stacks:1.40--1</container>
8 <yield/>
9 </requirements>
10 </xml>
11
12 <token name="@WRAPPER_VERSION@">1.40</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://creskolab.uoregon.edu/stacks/>`_
42
43 `Stacks manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_
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 </xml>
90
91 <xml name="cross_types">
92 <option value="CP">CP (F1 cross)</option>
93 <option value="F2">F2 (F2 cross)</option>
94 <option value="BC1">BC1 (backcross)</option>
95 <option value="DH">DH (double haploid cross)</option>
96 <option value="GEN">GEN (generic, unspecific to any map type)</option>
97 </xml>
98
99 <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@">
100 <![CDATA[
101 ## We need to do this as the output file names contains the value of an option (min progeny)
102 &&
103 cd stacks_outputs/ &&
104 ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv &&
105 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
106 ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt &&
107 ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv &&
108 cd ..
109 ]]>
110 </token>
111
112 <token name="@NORM_GENOTYPES_OUTPUT_FULL@">
113 <![CDATA[
114 ## We need to do this as the output file names contains the value of an option (min progeny)
115 &&
116 cd stacks_outputs/ &&
117 ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv &&
118 ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt &&
119 ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv &&
120 ln -s batch_1.genotypes_1.rqtl.tsv batch_1.genotypes.rqtl.tsv &&
121 ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv &&
122 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
123 ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt &&
124 ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv &&
125 cd ..
126 ]]>
127 </token>
128
129 <xml name="genotypes_output_light">
130
131 <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">
132 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
133 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter>
134 </data>
135
136 <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">
137 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
138 </data>
139 <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">
140 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
141 <filter>options_usage['cross_type'] == "GEN"</filter>
142 </data>
143
144 <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">
145 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
146 </data>
147
148 <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">
149 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
150 </data>
151 </xml>
152
153 <xml name="genotypes_output_full">
154 <!-- Output formats generated by genotypes:
155
156 JoinMap, default, only if map type is F2/BC1/DH/CP => batch_1.genotypes_1.loc
157 OneMap, only if map type is F2/BC1 => batch_1.genotypes_1onemap.tsv
158 OneMap/MapMaker, only if map type is CP => batch_1.genotypes_1.onemap.txt
159 Genomic, for all map types => batch_1.genomic_1.tsv
160 R/QTL, only if map type is F2/BC1/DH => batch_1.genotypes_1.rqtl.tsv
161
162 Additional non-optional output (ie not altered by -o option):
163
164 Generic format, for every map types => batch_1.haplotypes_1.tsv
165 Generic format, if map type is GEN => batch_1.genotypes_1.tsv -->
166
167 <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">
168 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter>
169 <filter>'map_out' not in options_usage or options_usage['map_out']['map_out_type'] == 'joinmap'</filter>
170 </data>
171
172 <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">
173 <filter>options_usage['cross_type'] in ['F2', 'BC1']</filter>
174 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter>
175 </data>
176
177 <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">
178 <filter>options_usage['cross_type'] in ['CP']</filter>
179 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter>
180 </data>
181
182 <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">
183 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'genomic'</filter>
184 </data>
185
186 <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">
187 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH']</filter>
188 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'rqtl'</filter>
189 </data>
190
191 <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"/>
192
193 <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">
194 <filter>options_usage['cross_type'] == "GEN"</filter>
195 </data>
196
197 <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"/>
198
199 <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"/>
200 </xml>
201
202 <xml name="populations_output_light">
203 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv">
204 <filter>options_usage['rad_analysis_type'] == "population"</filter>
205 </data>
206
207 <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">
208 <filter>options_usage['rad_analysis_type'] == "population"</filter>
209 </data>
210
211 <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">
212 <filter>options_usage['rad_analysis_type'] == "population"</filter>
213 </data>
214
215 <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">
216 <filter>options_usage['rad_analysis_type'] == "population"</filter>
217 </data>
218
219 <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">
220 <filter>options_usage['rad_analysis_type'] == "population"</filter>
221 </data>
222
223 <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">
224 <filter>options_usage['rad_analysis_type'] == "population"</filter>
225 </data>
226 </xml>
227
228 <xml name="populations_output_full">
229 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/>
230
231 <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"/>
232
233 <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"/>
234
235 <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"/>
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
239 <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"/>
240
241 <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">
242 <filter>fstats</filter>
243 </data>
244 <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">
245 <filter>populations_output['fasta']</filter>
246 </data>
247 <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">
248 <filter>populations_output['phylip_var_all']</filter>
249 </data>
250 <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">
251 <filter>populations_output['phylip_var_all']</filter>
252 </data>
253 <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">
254 <filter>populations_output['phylip_var_all']</filter>
255 </data>
256 <data format="tabular" name="out_genepop" label="GenePop formatwith ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genepop">
257 <filter>populations_output['genepop']</filter>
258 </data>
259 <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">
260 <filter>populations_output['vcf_haplotypes']</filter>
261 </data>
262 <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">
263 <filter>populations_output['hzar']</filter>
264 </data>
265 <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">
266 <filter>populations_output['beagle_phased']</filter>
267 </data>
268 <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">
269 <filter>populations_output['beagle_phased']</filter>
270 </data>
271 <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">
272 <filter>populations_output['beagle']</filter>
273 </data>
274 <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">
275 <filter>populations_output['beagle']</filter>
276 </data>
277 <data format="tabular" name="out_phylip_pop" label="Phylip (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip">
278 <filter>populations_output['phylip']</filter>
279 </data>
280 <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">
281 <filter>populations_output['phylip']</filter>
282 </data>
283 <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">
284 <filter>populations_output['plink']</filter>
285 </data>
286 <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">
287 <filter>populations_output['plink']</filter>
288 </data>
289 <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">
290 <filter>populations_output['fasta_strict']</filter>
291 </data>
292 <data format="tabular" name="out_structure" label="Structure format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.structure.tsv">
293 <filter>populations_output['structure']</filter>
294 </data>
295 <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">
296 <filter>populations_output['treemix']</filter>
297 </data>
298 <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">
299 <filter>populations_output['treemix']</filter>
300 </data>
301 <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">
302 <filter>populations_output['fastphase']</filter>
303 </data>
304 <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">
305 <filter>populations_output['phase']</filter>
306 </data>
307 <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">
308 <filter>populations_output['vcf']</filter>
309 </data>
310 <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">
311 <filter>populations_output['options_genomic']['genomic']</filter>
312 </data>
313
314 </xml>
315
316 <xml name="snp_options">
317 <conditional name="select_model">
318 <param name="model_type" type="select" label="Choose the model">
319 <option value="snp" selected="true">SNP</option>
320 <option value="bounded">Bounded SNP</option>
321 <option value="fixed">Fixed</option>
322 </param>
323 <when value="snp">
324 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
325 <option value="0.1">0.1</option>
326 <option value="0.05" selected="True">0.05</option>
327 <option value="0.01">0.01</option>
328 <option value="0.001">0.001</option>
329 </param>
330 </when>
331 <when value="bounded">
332 <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"/>
333 <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" />
334 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
335 <option value="0.1">0.1</option>
336 <option value="0.05" selected="True">0.05</option>
337 <option value="0.01">0.01</option>
338 <option value="0.001">0.001</option>
339 </param>
340 </when>
341 <when value="fixed">
342 </when>
343 </conditional>
344 </xml>
345
346 <xml name="snp_options_full">
347 <conditional name="select_model">
348 <param name="model_type" type="select" label="Choose the model">
349 <option value="snp" selected="true">SNP</option>
350 <option value="bounded">Bounded SNP</option>
351 <option value="fixed">Fixed</option>
352 </param>
353 <when value="snp">
354 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
355 <option value="0.1">0.1</option>
356 <option value="0.05" selected="True">0.05</option>
357 <option value="0.01">0.01</option>
358 <option value="0.001">0.001</option>
359 </param>
360 </when>
361 <when value="bounded">
362 <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"/>
363 <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" />
364 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
365 <option value="0.1">0.1</option>
366 <option value="0.05" selected="True">0.05</option>
367 <option value="0.01">0.01</option>
368 <option value="0.001">0.001</option>
369 </param>
370 </when>
371 <when value="fixed">
372 <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"/>
373 </when>
374 </conditional>
375 </xml>
376 </macros>