Mercurial > repos > iuc > stacks2_populations

comparison stacks_populations.xml @ 3:b242deb58952 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Thu, 16 Jul 2020 07:32:42 -0400
parents 38942a7e3801
children 887cf585cafc
comparison
equal deleted inserted replaced
2:38942a7e3801 3:b242deb58952
49 49
50 --min-populations $options_filtering.minpop 50 --min-populations $options_filtering.minpop
51 --min-samples-per-pop $options_filtering.minperc 51 --min-samples-per-pop $options_filtering.minperc
52 --min-samples-overall $options_filtering.min_samples_overall 52 --min-samples-overall $options_filtering.min_samples_overall
53 $options_filtering.filter_haplotype_wise 53 $options_filtering.filter_haplotype_wise
54 --min_maf $options_filtering.min_maf 54 --min-maf $options_filtering.min_maf
55 --min_mac $options_filtering.min_mac 55 --min-mac $options_filtering.min_mac
56 #if str($options_filtering.max_obs_het) 56 #if str($options_filtering.max_obs_het)
57 --max_obs_het $options_filtering.max_obs_het 57 --max-obs-het $options_filtering.max_obs_het
58 #end if 58 #end if
59 ## deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ 59 ## deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
60 ## #if str($options_filtering.lnl) 60 ## #if str($options_filtering.lnl)
61 ## --lnl_lim $options_filtering.lnl 61 ## --lnl-lim $options_filtering.lnl
62 ## #end if 62 ## #end if
63 $options_filtering.filter_single_snp 63 $options_filtering.filter_single_snp
64 #if $options_filtering.blacklist 64 #if $options_filtering.blacklist
65 -B '$options_filtering.blacklist' 65 -B '$options_filtering.blacklist'
66 #end if 66 #end if
71 ## Merging and Phasing: 71 ## Merging and Phasing:
72 #if str($merge_phase.enzyme) != '': 72 #if str($merge_phase.enzyme) != '':
73 -e $merge_phase.enzyme 73 -e $merge_phase.enzyme
74 #end if 74 #end if
75 $merge_phase.merge_sites 75 $merge_phase.merge_sites
76 --merge_prune_lim $merge_phase.merge_prune_lim 76 --merge-prune-lim $merge_phase.merge_prune_lim
77 77
78 ## Locus stats: 78 ## Locus stats:
79 $locus_stats.hwe 79 $locus_stats.hwe
80 80
81 ## Fstats 81 ## Fstats
82 #if str($fstats_conditional.fstats) != 'no': 82 #if str($fstats_conditional.fstats) != 'no':
83 --fstats 83 --fstats
84 #if str( $fstats_conditional.correction_select.fst_correction ) != "no_corr" 84 $fstats_conditional.fst_correction
85 --fst_correction $fstats_conditional.correction_select.fst_correction 85 #if $fstats_conditional.fst_correction
86 --p_value_cutoff $fstats_conditional.correction_select.p_value_cutoff 86 --p-value-cutoff $fstats_conditional.p_value_cutoff
87 #end if 87 #end if
88 #end if 88 #end if
89 89
90 ## Kernel-smoothing algorithm: 90 ## Kernel-smoothing algorithm:
91 $kernel_smoothing.options_kernel.kernel 91 $kernel_smoothing.options_kernel.kernel
101 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist 101 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist
102 #end if 102 #end if
103 103
104 #if $kernel_smoothing.bootstrap_resampling_mode.bootstrap or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_pifis or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_fst or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_div or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist: 104 #if $kernel_smoothing.bootstrap_resampling_mode.bootstrap or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_pifis or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_fst or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_div or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist:
105 #if str($kernel_smoothing.bootstrap_reps) 105 #if str($kernel_smoothing.bootstrap_reps)
106 --bootstrap_reps $kernel_smoothing.bootstrap_reps 106 --bootstrap-reps $kernel_smoothing.bootstrap_reps
107 #end if 107 #end if
108 #if $kernel_smoothing.bootstrap_wl 108 #if $kernel_smoothing.bootstrap_wl
109 --bootstrap_wl '$kernel_smoothing.bootstrap_wl' 109 --bootstrap-wl '$kernel_smoothing.bootstrap_wl'
110 #end if 110 #end if
111 #end if 111 #end if
112 112
113 ## File output options: 113 ## File output options:
114 114
128 ##$populations_output.phylip_var_all 128 ##$populations_output.phylip_var_all
129 $populations_output.treemix 129 $populations_output.treemix
130 $populations_output.no_hap_exports 130 $populations_output.no_hap_exports
131 $populations_output.fasta_samples_raw 131 $populations_output.fasta_samples_raw
132 132
133 #if $genetic_map_options.map_type:
134 --map-type $genetic_map_options.map_type
135 #end if
136 #if $genetic_map_options.map_format
137 --map-format $genetic_map_options.map_format
138 #end if
139
133 ## Additional options: 140 ## Additional options:
134 141
135 $advanced_options.log_fst_comp 142 $advanced_options.log_fst_comp
136 143
137 ## populations outputs log info to stdout for vcf input 144 ## populations outputs log info to stdout for vcf input
144 #if $output_log 151 #if $output_log
145 > $output_log 152 > $output_log
146 #end if 153 #end if
147 && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done 154 && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done
148 #end if 155 #end if
156
157 ## move the genotype output (note that in 2.52 there is an inconsistent
158 ## naming for onemap output and also extensions are inconsistent -> therefore wildcard)
159 #if $genetic_map_options.map_type and $genetic_map_options.map_format
160 && mv stacks_outputs/populations.${genetic_map_options.map_type}.* stacks_outputs/populations.sql.tsv
161 #end if
149 ]]></command> 162 ]]></command>
150 163
151 <inputs> 164 <inputs>
152 <conditional name="options_usage"> 165 <conditional name="options_usage">
153 <param name="input_type" type="select" label="Input type" help="select input file type" > 166 <param name="input_type" type="select" label="Input type" help="select input file type" >
156 </param> 169 </param>
157 <when value="stacks"> 170 <when value="stacks">
158 <expand macro="input_aln_macro"/> 171 <expand macro="input_aln_macro"/>
159 </when> 172 </when>
160 <when value="vcf"> 173 <when value="vcf">
161 <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" /> 174 <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V"/>
162 </when> 175 </when>
163 </conditional> 176 </conditional>
164 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" help="Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'." optional="true"/> 177 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" help="Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'." optional="true"/>
165 <param argument="--batch_size" type="integer" value="" optional="true" label="Number of loci to process in a batch" help="(default: 10,000 in de novo mode; in reference mode, one chromosome per batch). Increase to speed analysis, uses more memory, decrease to save memory)"/> 178 <param argument="--batch-size" type="integer" value="" optional="true" label="Number of loci to process in a batch" help="(default: 10,000 in de novo mode; in reference mode, one chromosome per batch). Increase to speed analysis, uses more memory, decrease to save memory)"/>
166 179
167 <!-- Data Filtering --> 180 <!-- Data Filtering -->
168 <section name="options_filtering" title="Data filtering options" expanded="true"> 181 <section name="options_filtering" title="Data filtering options" expanded="true">
169 182
170 <param name="minperc" argument="--min-samples-per-pop" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" /> 183 <param name="minperc" argument="--min-samples-per-pop" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population"/>
171 <param name="minpop" argument="--min-populations" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus" /> 184 <param name="minpop" argument="--min-populations" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus"/>
172 <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus" /> 185 <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus"/>
173 <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data." /> 186 <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data."/>
174 <param argument="--min_maf" type="float" value="0" min="0" max="0.5" label="Minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus" /> 187 <param argument="--min-maf" type="float" value="0" min="0" max="0.5" label="Minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus"/>
175 <param argument="--min_mac" type="integer" value="0" min="0" label="Minimum minor allele count" help="specify a minimum minor allele count required to process a nucleotide site at a locus" /> 188 <param argument="--min-mac" type="integer" value="0" min="0" label="Minimum minor allele count" help="specify a minimum minor allele count required to process a nucleotide site at a locus"/>
176 <param argument="--max_obs_het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus." /> 189 <param argument="--max-obs-het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus."/>
177 <!-- deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ 190 <!-- deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
178 <param type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold" />--> 191 <param type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold"/>-->
179 <param name="filter_single_snp" type="select" label="Analyse all SNPs per locus" > 192 <param name="filter_single_snp" type="select" label="Analyse all SNPs per locus" >
180 <option value="">yes</option> 193 <option value="">yes</option>
181 <option value="--write_single_snp">No: Analyse only the first SNP (--write_single_snp)</option> 194 <option value="--write-single-snp">No: Analyse only the first SNP (--write-single-snp)</option>
182 <option value="--write_random_snp">No: Analyse only one random SNP (--write_random_snp)</option> 195 <option value="--write-random-snp">No: Analyse only one random SNP (--write-random-snp)</option>
183 </param> 196 </param>
184 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export" /> 197 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export"/>
185 <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export" /> 198 <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export"/>
186 </section> 199 </section>
187 200
188 <!-- merging and Phasing --> 201 <!-- merging and Phasing -->
189 <section name="merge_phase" title="Merging and Phasing" expanded="true"> 202 <section name="merge_phase" title="Merging and Phasing" expanded="true">
190 <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" > 203 <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" >
191 <expand macro="enzymes"/> 204 <expand macro="enzymes"/>
192 </param> 205 </param>
193 <param argument="--merge_sites" truevalue="--merge_sites" falsevalue="" type="boolean" checked="false" label="Merge loci that were produced from the same restriction enzyme cutsite" help="(requires reference-aligned data)" /> 206 <param argument="--merge-sites" truevalue="--merge-sites" falsevalue="" type="boolean" checked="false" label="Merge loci that were produced from the same restriction enzyme cutsite" help="(requires reference-aligned data)"/>
194 <param argument="--merge_prune_lim" type="float" value="1.0" min="0.0" max="1.0" label="Fraction of samples possessing both loci to prune remaining samples from analysis" help="for merging adjacent loci"/> 207 <param argument="--merge-prune-lim" type="float" value="1.0" min="0.0" max="1.0" label="Fraction of samples possessing both loci to prune remaining samples from analysis" help="for merging adjacent loci"/>
195 </section> 208 </section>
196 209
197 <!-- Locus stats --> 210 <!-- Locus stats -->
198 <section name="locus_stats" title="Locus Stats" expanded="true"> 211 <section name="locus_stats" title="Locus Stats" expanded="true">
199 <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="Calculate divergence from Hardy-Weinberg equilibrium for each locus" /> 212 <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="Calculate divergence from Hardy-Weinberg equilibrium for each locus"/>
200 </section> 213 </section>
201 214
202 <!-- Fstats --> 215 <!-- Fstats -->
203 <conditional name="fstats_conditional"> 216 <conditional name="fstats_conditional">
204 <param argument="--fstats" type="select" label="Enable SNP and haplotype-based F statistics" > 217 <param argument="--fstats" type="select" label="Enable SNP and haplotype-based F statistics" >
205 <option value="no">No</option> 218 <option value="no">No</option>
206 <option value="yes">Yes</option> 219 <option value="yes">Yes</option>
207 </param> 220 </param>
208 <when value="no"/> 221 <when value="no"/>
209 <when value="yes"> 222 <when value="yes">
210 <conditional name="correction_select"> 223 <param argument="--fst-correction" truevalue="--fst-correction" falsevalue="" type="boolean" checked="false" label="apply a p-value correction to Fst values based on a Fisher's exact test" help=""/>
211 <param argument="--fst_correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values" > 224 <param argument="--p-value-cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default)."/>
212 <option value="no_corr">No correction</option>
213 <option value="p_value">p_value</option>
214 <option value="bonferroni_win">bonferroni_win</option>
215 <option value="bonferroni_gen">bonferroni_gen</option>
216 </param>
217 <when value="no_corr"/>
218 <when value="p_value">
219 <param argument="--p_value_cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
220 </when>
221 <when value="bonferroni_win">
222 <param argument="--p_value_cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
223 </when>
224 <when value="bonferroni_gen">
225 <param argument="--p_value_cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
226 </when>
227 </conditional>
228 </when> 225 </when>
229 </conditional> 226 </conditional>
230 227
231 <!-- File output options --> 228 <!-- File output options -->
232 <section name="populations_output" title="Output options" expanded="true"> 229 <section name="populations_output" title="Output options" expanded="true">
233 <param argument="--ordered_export" truevalue="--ordered_export" falsevalue="" type="boolean" checked="false" label="If data is reference aligned, exports will be ordered; only a single representative of each overlapping site." /> 230 <param argument="--ordered-export" truevalue="--ordered-export" falsevalue="" type="boolean" checked="false" label="If data is reference aligned, exports will be ordered; only a single representative of each overlapping site."/>
234 <param argument="--fasta_loci" truevalue="--fasta_loci" falsevalue="" type="boolean" checked="false" label="Output locus consensus sequences in FASTA format" /> 231 <param argument="--fasta-loci" truevalue="--fasta-loci" falsevalue="" type="boolean" checked="false" label="Output locus consensus sequences in FASTA format"/>
235 <param argument="--fasta_samples" truevalue="--fasta_samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format" /> 232 <param argument="--fasta-samples" truevalue="--fasta-samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format"/>
236 <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" /> 233 <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/>
237 <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" /> 234 <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/>
238 <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" /> 235 <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/>
239 <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format" /> 236 <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/>
240 <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" />--> 237 <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format"/>-->
241 <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" /> 238 <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format"/>
242 <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" /> 239 <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/>
243 <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." /> 240 <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/>
244 <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction" /> 241 <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/>
245 <param argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." /> 242 <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/>
246 <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip_var_all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation." />--> 243 <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip-var-all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation."/>-->
247 <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)." /> 244 <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)."/>
248 <param argument="--no_hap_exports" truevalue="--no_hap_exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs" /> 245 <param argument="--no-hap-exports" truevalue="--no-hap-exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs"/>
249 <param argument="--fasta_samples_raw" truevalue="--fasta_samples_raw" falsevalue="" type="boolean" checked="false" label="Output all haplotypes observed in each sample, for each locus, in FASTA format" /> 246 <param argument="--fasta-samples-raw" truevalue="--fasta-samples-raw" falsevalue="" type="boolean" checked="false" label="Output all haplotypes observed in each sample, for each locus, in FASTA format"/>
250 </section> 247 </section>
251 248
252 <!-- Kernel-smoothing algorithm --> 249 <!-- Kernel-smoothing algorithm -->
253 <section name="kernel_smoothing" title="Kernel smoothing" expanded="false"> 250 <section name="kernel_smoothing" title="Kernel smoothing" expanded="false">
254 <conditional name="options_kernel"> 251 <conditional name="options_kernel">
255 <param name="kernel" type="select" label="Enable kernel-smoothed calculations" > 252 <param name="kernel" type="select" label="Enable kernel-smoothed calculations" >
256 <option value="">No</option> 253 <option value="">No</option>
257 <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</option> 254 <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</option>
258 <option value="--smooth_fstats">For Fst, Fst', and Phi_st (--smooth_fstats)</option> 255 <option value="--smooth-fstats">For Fst, Fst', and Phi_st (--smooth-fstats)</option>
259 <option value="--smooth_popstats">For Pi and Fis (--smooth_popstats)</option> 256 <option value="--smooth-popstats">For Pi and Fis (--smooth-popstats)</option>
260 </param> 257 </param>
261 <when value=""/> 258 <when value=""/>
262 <when value="-k"> 259 <when value="-k">
263 <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" /> 260 <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)"/>
264 </when> 261 </when>
265 <when value="--smooth_fstats"> 262 <when value="--smooth-fstats">
266 <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" /> 263 <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)"/>
267 </when> 264 </when>
268 <when value="--smooth_popstats"> 265 <when value="--smooth-popstats">
269 <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" /> 266 <param argument="--sigma" type="float" value="150000" label="Standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)"/>
270 </when> 267 </when>
271 </conditional> 268 </conditional>
272 <conditional name="bootstrap_resampling_mode"> 269 <conditional name="bootstrap_resampling_mode">
273 <param argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics" > 270 <param argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics" >
274 <option value="">No</option> 271 <option value="">No</option>
275 <option value="--bootstrap">Yes</option> 272 <option value="--bootstrap">Yes</option>
276 </param> 273 </param>
277 <when value="--bootstrap"> 274 <when value="--bootstrap">
278 </when> 275 </when>
279 <when value=""> 276 <when value="">
280 <param argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" /> 277 <param argument="--bootstrap-pifis" type="boolean" checked="false" truevalue="--bootstrap-pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations"/>
281 <param argument="--bootstrap_fst" type="boolean" checked="false" truevalue="--bootstrap_fst" falsevalue="" label="Enable boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs" /> 278 <param argument="--bootstrap-fst" type="boolean" checked="false" truevalue="--bootstrap-fst" falsevalue="" label="Enable boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs"/>
282 <param argument="--bootstrap_div" type="boolean" checked="false" truevalue="--bootstrap_div" falsevalue="" label="Enable boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes" /> 279 <param argument="--bootstrap-div" type="boolean" checked="false" truevalue="--bootstrap-div" falsevalue="" label="Enable boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes"/>
283 <param argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." /> 280 <param argument="--bootstrap-phist" type="boolean" checked="false" truevalue="--bootstrap-phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes."/>
284 </when> 281 </when>
285 </conditional> 282 </conditional>
286 <param argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" /> 283 <param argument="--bootstrap-reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate"/>
287 <param argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" /> 284 <param argument="--bootstrap-wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist"/>
288 </section> 285 </section>
289 286
290 <!-- Output options --> 287 <!-- Output options -->
291 <section name="advanced_options" title="Advanced options" expanded="False"> 288 <section name="advanced_options" title="Advanced options" expanded="False">
292 <param argument="--log_fst_comp" type="boolean" checked="false" truevalue="--log_fst_comp" falsevalue="" label="Log components of Fst/Phi_st calculations to a dataset" /> 289 <param argument="--log-fst-comp" type="boolean" checked="false" truevalue="--log-fst-comp" falsevalue="" label="Log components of Fst/Phi_st calculations to a dataset"/>
290 </section>
291
292 <!-- Genetic map output options (population map must specify a genetic cross): -->
293 <section name="genetic_map_options" title="Genetic map output options (population map must specify a genetic cross)" help="works only if a population map specifying only two groupings: 'parent' and 'progeny'" expanded="false">
294 <param argument="--map-type" type="select" optional="true" label="genetic map type to write" help="needs to be selected to trigger the additional Genotyping markers output">
295 <option value="CP">CP</option>
296 <option value="DH">DH</option>
297 <option value="F2">F2</option>
298 <option value="BC1">BC1</option>
299 </param>
300 <param argument="--map-format" type="select" optional="true" label="mapping program format to write" help="needs to be selected to trigger the additional Genotyping markers output">
301 <option value="joinmap">joinmap</option>
302 <option value="onemap">onemap</option>
303 <option value="rqtl">rqtl</option>
304 </param>
293 </section> 305 </section>
294 <expand macro="in_log"/> 306 <expand macro="in_log"/>
295 </inputs> 307 </inputs>
296 <outputs> 308 <outputs>
297 <expand macro="out_log"/> 309 <expand macro="out_log"/>
298 <expand macro="populations_output_full"/> 310 <expand macro="populations_output_full"/>
299 </outputs> 311 </outputs>
300
301 <tests> 312 <tests>
302 <!-- test w gstacks output as input and default options --> 313 <!-- test w gstacks output as input and default options -->
303 <test> 314 <test expect_num_outputs="6">
304 <param name="options_usage|input_type" value="stacks" /> 315 <param name="options_usage|input_type" value="stacks"/>
305 <param name="options_usage|input_aln"> 316 <param name="options_usage|input_aln">
306 <collection type="list"> 317 <collection type="list">
307 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> 318 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
308 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> 319 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
309 </collection> 320 </collection>
310 </param> 321 </param>
311 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 322 <param name="batch_size" value="9999"/>
312 <param name="batch_size" value="9999" /> 323 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
313 <param name="add_log" value="yes" /> 324 <param name="batch_size" value="9999"/>
325 <param name="add_log" value="yes"/>
314 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/> 326 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
315 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> 327 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
316 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> 328 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
317 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/> 329 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
318 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> 330 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
319 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> 331 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
320 <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
321 </test> 332 </test>
322 <!-- test w gstacks output as input, wo popmap, and default options --> 333 <!-- test w gstacks output as input, wo popmap, and default options -->
323 <test> 334 <test expect_num_outputs="6">
324 <param name="options_usage|input_type" value="stacks" /> 335 <param name="options_usage|input_type" value="stacks"/>
325 <param name="options_usage|input_aln"> 336 <param name="options_usage|input_aln">
326 <collection type="list"> 337 <collection type="list">
327 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> 338 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
328 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> 339 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
329 </collection> 340 </collection>
330 </param> 341 </param>
331 <param name="add_log" value="yes" /> 342 <param name="add_log" value="yes"/>
332 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 343 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
333 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> 344 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
334 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> 345 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
335 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> 346 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
336 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> 347 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
337 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> 348 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
338 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output>
339 </test> 349 </test>
340 <!-- test w gstacks output as input and + all outputs --> 350 <!-- test w gstacks output as input and + all outputs -->
341 <test> 351 <test expect_num_outputs="26">
342 <param name="options_usage|input_type" value="stacks" /> 352 <param name="options_usage|input_type" value="stacks"/>
343 <param name="options_usage|input_aln"> 353 <param name="options_usage|input_aln">
344 <collection type="list"> 354 <collection type="list">
345 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> 355 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
346 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> 356 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
347 </collection> 357 </collection>
348 </param> 358 </param>
349 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 359 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
350 <param name="add_log" value="yes" /> 360 <param name="add_log" value="yes"/>
351 <param name="advanced_options|log_fst_comp" value="yes"/> 361 <param name="advanced_options|log_fst_comp" value="yes"/>
352 <param name="fstats_conditional|fstats" value="yes"/> 362 <param name="fstats_conditional|fstats" value="yes"/>
353 <param name="populations_output|fasta_loci" value="yes"/> 363 <param name="populations_output|fasta_loci" value="yes"/>
354 <param name="populations_output|fasta_samples" value="yes"/> 364 <param name="populations_output|fasta_samples" value="yes"/>
355 <param name="populations_output|fasta_samples_raw" value="yes"/> 365 <param name="populations_output|fasta_samples_raw" value="yes"/>
361 <param name="populations_output|plink" value="yes"/> 371 <param name="populations_output|plink" value="yes"/>
362 <param name="populations_output|structure" value="yes"/> 372 <param name="populations_output|structure" value="yes"/>
363 <param name="populations_output|radpainter" value="yes"/> 373 <param name="populations_output|radpainter" value="yes"/>
364 <param name="populations_output|treemix" value="yes"/> 374 <param name="populations_output|treemix" value="yes"/>
365 <assert_command> 375 <assert_command>
366 <has_text text="--log_fst_comp" /> 376 <has_text text="--log-fst-comp"/>
367 </assert_command> 377 </assert_command>
368 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 378 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
369 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> 379 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
370 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> 380 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
371 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/> 381 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/>
372 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> 382 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
373 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> 383 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
374 <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
375 384
376 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> 385 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
377 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> 386 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
378 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> 387 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
379 <output ftype="tabular" name="out_fasta_strict" value="populations/populations.loci.fa" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header --> 388 <output ftype="tabular" name="out_fasta_strict" value="populations/populations.loci.fa" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header -->
380 <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " --> 389 <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " -->
381 <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " --> 390 <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " -->
382 <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/><!-- " --> 391 <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/><!-- " -->
383 <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/> 392 <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/>
384 <output ftype="tabular" name="out_phylip_all_pop_var" value="populations/populations.var.phylip" compare="sim_size" delta="50"/> 393 <output ftype="tabular" name="out_phylip_all_pop_var" value="populations/populations.var.phylip" compare="sim_size" delta="50"/>
385 <output ftype="tabular" name="out_phylip_all_loci_var" value="populations/populations.var.phylip.log" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header --> 394 <output ftype="tabular" name="out_phylip_all_loci_var" value="populations/populations.var.phylip.log" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header -->
393 <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " --> 402 <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " -->
394 <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " --> 403 <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " -->
395 <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " --> 404 <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " -->
396 </test> 405 </test>
397 <!-- test w vcf input and default options, just checking if finished --> 406 <!-- test w vcf input and default options, just checking if finished -->
398 <test> 407 <test expect_num_outputs="6">
399 <param name="options_usage|input_type" value="vcf" /> 408 <param name="options_usage|input_type" value="vcf"/>
400 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> 409 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
401 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 410 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
402 <param name="add_log" value="yes" /> 411 <param name="add_log" value="yes"/>
403 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 412 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
404 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> 413 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
405 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> 414 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
406 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> 415 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
407 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> 416 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
408 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> 417 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
409 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output>
410 </test> 418 </test>
411 <!-- test w gstacks output as input and non default filtering --> 419 <!-- test w gstacks output as input and non default filtering -->
412 <test> 420 <test expect_num_outputs="6">
413 <param name="options_usage|input_type" value="stacks" /> 421 <param name="options_usage|input_type" value="stacks"/>
414 <param name="options_usage|input_aln"> 422 <param name="options_usage|input_aln">
415 <collection type="list"> 423 <collection type="list">
416 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> 424 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
417 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> 425 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
418 </collection> 426 </collection>
419 </param> 427 </param>
420 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 428 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
421 <param name="add_log" value="yes" /> 429 <param name="add_log" value="yes"/>
422 <section name="options_filtering"> 430 <section name="options_filtering">
423 <param name="minperc" value="0.1"/> 431 <param name="minperc" value="0.1"/>
424 <param name="minpop" value="2"/> 432 <param name="minpop" value="2"/>
425 <param name="min_samples_overall" value="0.01"/> 433 <param name="min_samples_overall" value="0.01"/>
426 <param name="filter_haplotype_wise" value="--filter-haplotype-wise"/> 434 <param name="filter_haplotype_wise" value="--filter-haplotype-wise"/>
427 <param name="min_maf" value="0.01" /> 435 <param name="min_maf" value="0.01"/>
428 <param name="min_mac" value="1"/> 436 <param name="min_mac" value="1"/>
429 <param name="max_obs_het" value="0.8" /> 437 <param name="max_obs_het" value="0.8"/>
430 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> 438 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/>
431 </section> 439 </section>
432 <assert_command> 440 <assert_command>
433 <has_text text="--min-samples-per-pop 0.1" /> 441 <has_text text="--min-samples-per-pop 0.1"/>
434 <has_text text="--min-populations 2" /> 442 <has_text text="--min-populations 2"/>
435 <has_text text="--min-samples-overall 0.01" /> 443 <has_text text="--min-samples-overall 0.01"/>
436 <has_text text="--filter-haplotype-wise" /> 444 <has_text text="--filter-haplotype-wise"/>
437 <has_text text="--min_maf 0.01" /> 445 <has_text text="--min-maf 0.01"/>
438 <has_text text="--min_mac 1" /> 446 <has_text text="--min-mac 1"/>
439 <has_text text="--max_obs_het 0.8" /> 447 <has_text text="--max-obs-het 0.8"/>
440 <has_text text="-B " /> 448 <has_text text="-B "/>
441 </assert_command> 449 </assert_command>
442 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 450 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
443 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> 451 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
444 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> 452 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
445 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> 453 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
446 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> 454 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
447 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> 455 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
448 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output>
449 </test> 456 </test>
450 <!-- test w gstacks output as input and non default filtering (needed because filter-haplotype-wise is incompatible with write_random_snp/write_single_snp) --> 457 <!-- test w gstacks output as input and non default filtering (needed because filter-haplotype-wise is incompatible with write_random_snp/write_single_snp) -->
451 <test> 458 <test expect_num_outputs="6">
452 <param name="options_usage|input_type" value="stacks" /> 459 <param name="options_usage|input_type" value="stacks"/>
453 <param name="options_usage|input_aln"> 460 <param name="options_usage|input_aln">
454 <collection type="list"> 461 <collection type="list">
455 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> 462 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
456 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> 463 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
457 </collection> 464 </collection>
458 </param> 465 </param>
459 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 466 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
460 <param name="add_log" value="yes" /> 467 <param name="add_log" value="yes"/>
461 <section name="options_filtering"> 468 <section name="options_filtering">
462 <param name="minperc" value="0.1"/> 469 <param name="minperc" value="0.1"/>
463 <param name="minpop" value="2"/> 470 <param name="minpop" value="2"/>
464 <param name="min_samples_overall" value="0.01"/> 471 <param name="min_samples_overall" value="0.01"/>
465 <param name="min_maf" value="0.01" /> 472 <param name="min_maf" value="0.01"/>
466 <param name="min_mac" value="1"/> 473 <param name="min_mac" value="1"/>
467 <param name="max_obs_het" value="0.8" /> 474 <param name="max_obs_het" value="0.8"/>
468 <!-- since write_random_snp runs in infinite loop switch to write_single --> 475 <!-- since write_random_snp runs in infinite loop switch to write_single -->
469 <param name="filter_single_snp" value="--write_single_snp"/> 476 <param name="filter_single_snp" value="--write-single-snp"/>
470 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> 477 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/>
471 </section> 478 </section>
472 <assert_command> 479 <assert_command>
473 <has_text text="--min-samples-per-pop 0.1" /> 480 <has_text text="--min-samples-per-pop 0.1"/>
474 <has_text text="--min-populations 2" /> 481 <has_text text="--min-populations 2"/>
475 <has_text text="--min-samples-overall 0.01" /> 482 <has_text text="--min-samples-overall 0.01"/>
476 <has_text text="--min_maf 0.01" /> 483 <has_text text="--min-maf 0.01"/>
477 <has_text text="--min_mac 1" /> 484 <has_text text="--min-mac 1"/>
478 <has_text text="--max_obs_het 0.8" /> 485 <has_text text="--max-obs-het 0.8"/>
479 <not_has_text text="--write_random_snp" /> 486 <not_has_text text="--write-random-snp"/>
480 <has_text text="-B " /> 487 <has_text text="-B "/>
481 </assert_command> 488 </assert_command>
482 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 489 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
483 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> 490 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
484 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> 491 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
485 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> 492 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
486 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> 493 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
487 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> 494 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
488 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output>
489 </test> 495 </test>
490 <!-- test w gstacks output as input and non default merging/hwe --> 496 <!-- test w gstacks output as input and non default merging/hwe -->
491 <test> 497 <test expect_num_outputs="6">
492 <param name="options_usage|input_type" value="stacks" /> 498 <param name="options_usage|input_type" value="stacks"/>
493 <param name="options_usage|input_aln"> 499 <param name="options_usage|input_aln">
494 <collection type="list"> 500 <collection type="list">
495 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> 501 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
496 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> 502 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
497 </collection> 503 </collection>
498 </param> 504 </param>
499 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 505 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
500 <section name="merge_phase"> 506 <section name="merge_phase">
501 <param name="enzyme" value="ecoRI"/> 507 <param name="enzyme" value="ecoRI"/>
502 <param name="merge_sites" value="yes"/> 508 <param name="merge_sites" value="yes"/>
503 <param name="merge_prune_lim" value="0.9" /> 509 <param name="merge_prune_lim" value="0.9"/>
504 </section> 510 </section>
505 <section name="locus_stats"> 511 <section name="locus_stats">
506 <param name="hwe" value="yes" /> 512 <param name="hwe" value="yes"/>
507 </section> 513 </section>
508 <param name="add_log" value="yes" /> 514 <param name="add_log" value="yes"/>
509 <assert_command> 515 <assert_command>
510 <has_text text="-e ecoRI" /> 516 <has_text text="-e ecoRI"/>
511 <has_text text="--merge_sites" /> 517 <has_text text="--merge-sites"/>
512 <has_text text="--merge_prune_lim 0.9" /> 518 <has_text text="--merge-prune-lim 0.9"/>
513 <has_text text="--hwe" /> 519 <has_text text="--hwe"/>
514 </assert_command> 520 </assert_command>
515 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 521 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
516 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> 522 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
517 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> 523 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
518 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> 524 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
519 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> 525 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
520 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> 526 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
521 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output>
522 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
523 </test> 527 </test>
524 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap --> 528 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
525 <test> 529 <test expect_num_outputs="6">
526 <param name="options_usage|input_type" value="stacks" /> 530 <param name="options_usage|input_type" value="stacks"/>
527 <param name="options_usage|input_aln"> 531 <param name="options_usage|input_aln">
528 <collection type="list"> 532 <collection type="list">
529 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf" /> 533 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/>
530 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz" /> 534 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/>
531 </collection> 535 </collection>
532 </param> 536 </param>
533 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 537 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
534 <conditional name="fstats_conditional"> 538 <conditional name="fstats_conditional">
535 <param name="fstats" value="yes" /> 539 <param name="fstats" value="yes"/>
536 <conditional name="correction_select"> 540 <param name="fst_correction" value="--fst-correction"/>
537 <param name="fst_correction" value="bonferroni_gen"/> 541 <param name="p_value_cutoff" value="0.01"/>
538 <param name="p_value_cutoff" value="0.01" />
539 </conditional>
540 </conditional> 542 </conditional>
541 <conditional name="options_kernel"> 543 <conditional name="options_kernel">
542 <param name="kernel" value="-k" /> 544 <param name="kernel" value="-k"/>
543 <param name="sigma" value="150001" /> 545 <param name="sigma" value="150001"/>
544 </conditional> 546 </conditional>
545 <conditional name="bootstrap_resampling_mode"> 547 <conditional name="bootstrap_resampling_mode">
546 <param name="bootstrap" value="--bootstrap" /> 548 <param name="bootstrap" value="--bootstrap"/>
547 </conditional> 549 </conditional>
548 <param name="bootstrap_reps" value="23" /> 550 <param name="bootstrap_reps" value="23"/>
549 <param name="add_log" value="yes" /> 551 <param name="add_log" value="yes"/>
550 <assert_command> 552 <assert_command>
551 <has_text text="--fstats" /> 553 <has_text text="--fstats"/>
552 <has_text text="--fst_correction bonferroni_gen" /> 554 <has_text text="--fst-correction"/>
553 <has_text text="--p_value_cutoff 0.01" /> 555 <has_text text="--p-value-cutoff 0.01"/>
554 <has_text text="-k " /> 556 <has_text text="-k "/>
555 <has_text text="--sigma 150001" /> 557 <has_text text="--sigma 150001"/>
556 <has_text text="--bootstrap" /> 558 <has_text text="--bootstrap"/>
557 <has_text text="--bootstrap_reps 23" /> 559 <has_text text="--bootstrap-reps 23"/>
558 </assert_command> 560 </assert_command>
559 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 561 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
560 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 562 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
561 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> 563 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
562 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> 564 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
563 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> 565 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
564 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> 566 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
565 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> 567 </test>
566 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output> 568 <!-- test w gstacks output as input and default options -->
569 <test expect_num_outputs="6">
570 <param name="options_usage|input_type" value="stacks"/>
571 <param name="options_usage|input_aln">
572 <collection type="list">
573 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
574 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
575 </collection>
576 </param>
577 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
578 <param name="add_log" value="yes"/>
579 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
580 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
581 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
582 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
583 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
584 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
585 </test>
586 <!-- test w gstacks output as input, wo popmap, and Genetic map output options that have been added in 2.5 -->
587 <test expect_num_outputs="7">
588 <param name="options_usage|input_type" value="stacks"/>
589 <param name="options_usage|input_aln">
590 <collection type="list">
591 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
592 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
593 </collection>
594 </param>
595 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks_genotypes.tsv"/>
596 <section name="genetic_map_options">
597 <param name="map_type" value="CP"/>
598 <param name="map_format" value="joinmap"/>
599 </section>
600 <param name="add_log" value="yes"/>
601 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
602 <output ftype="txt" name="out_sql" file="populations/populations.CP.joinmap.loc" lines_diff="4"/>
603 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
604 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
605 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
606 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
607 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
567 </test> 608 </test>
568 </tests> 609 </tests>
569 <help> 610 <help>
570 <![CDATA[ 611 <![CDATA[
571 .. class:: infomark 612 .. class:: infomark
623 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 664 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
624 665
625 @STACKS_INFOS@ 666 @STACKS_INFOS@
626 ]]> 667 ]]>
627 </help> 668 </help>
628 <expand macro="citation" /> 669 <expand macro="citation"/>
629 </tool> 670 </tool>