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comparison stacks_populations.xml @ 12:d1fad35bdb4a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 22:00:26 +0000
parents 95286af4139b
children
comparison
equal deleted inserted replaced
11:95286af4139b 12:d1fad35bdb4a
1 <tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.2"> 1 <tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.3">
2 <description>analyze a population of individual samples ('populations' program)</description> 2 <description>analyze a population of individual samples ('populations' program)</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #import re 10 #import re
11 11
18 #set $filename = str($input_file.element_identifier) 18 #set $filename = str($input_file.element_identifier)
19 #if not $filename.endswith('.tsv') 19 #if not $filename.endswith('.tsv')
20 #set $filename = $filename + ".tsv" 20 #set $filename = $filename + ".tsv"
21 #end if 21 #end if
22 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename) 22 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename)
23 ln -s '${input_file}' 'stacks_outputs/${filename}' && 23 cp '${input_file}' 'stacks_outputs/${filename}' &&
24 #end if 24 #end if
25 #end for 25 #end for
26 #else if str($options_usage.input_type) == 'vcf' 26 #else if str($options_usage.input_type) == 'vcf'
27 ln -s '$options_usage.input_vcf' 'stacks_outputs/batch_1.vcf' && 27 cp '$options_usage.input_vcf' 'stacks_outputs/batch_1.vcf' &&
28 #end if 28 #end if
29 29
30 populations 30 populations
31 31
32 -t \${GALAXY_SLOTS:-1} 32 -t \${GALAXY_SLOTS:-1}
64 #end if 64 #end if
65 65
66 ## Fstats 66 ## Fstats
67 $fstats 67 $fstats
68 68
69 #if $options_kernel.kernel 69 #if $options_kernel.kernel != ""
70 -k 70 -k
71 --sigma $options_kernel.sigma 71 --sigma $options_kernel.sigma
72 #end if 72 #end if
73 73
74 ## Bootstrap resampling options 74 ## Bootstrap resampling options
75 #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all 75 #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all != ""
76 --bootstrap 76 --bootstrap
77 #else 77 #else
78 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_pifis 78 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_pifis
79 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_fst 79 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_fst
80 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_div 80 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_div
105 $populations_output.phylip 105 $populations_output.phylip
106 $populations_output.phylip_var 106 $populations_output.phylip_var
107 $populations_output.phylip_var_all 107 $populations_output.phylip_var_all
108 $populations_output.treemix 108 $populations_output.treemix
109 109
110 #if $populations_output.options_genomic.genomic 110 #if $populations_output.options_genomic.genomic != ''
111 --genomic 111 --genomic
112 -e $populations_output.options_genomic.enzyme 112 -e $populations_output.options_genomic.enzyme
113 #end if 113 #end if
114 114
115 ## output SQL file (as denovo/refmap) and fst/phi components 115 ## output SQL file (as denovo/refmap) and fst/phi components
149 149
150 <param name="minperc" argument="-r" type="float" value="0.5" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" /> 150 <param name="minperc" argument="-r" type="float" value="0.5" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" />
151 <param name="minpop" argument="-p" type="integer" value="2" label="Minimum number of populations a locus must be present in to process a locus" /> 151 <param name="minpop" argument="-p" type="integer" value="2" label="Minimum number of populations a locus must be present in to process a locus" />
152 <param name="mindepth" argument="-m" type="integer" value="1" label="Specify a minimum stack depth required for individuals at a locus" /> 152 <param name="mindepth" argument="-m" type="integer" value="1" label="Specify a minimum stack depth required for individuals at a locus" />
153 <param name="minminor" argument="--min_maf" type="float" value="0.25" label="Specify a minimum minor allele frequency required before calculating Fst at a locus (between 0 and 0.5)" /> 153 <param name="minminor" argument="--min_maf" type="float" value="0.25" label="Specify a minimum minor allele frequency required before calculating Fst at a locus (between 0 and 0.5)" />
154 <param name="max_obs_het" 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." /> 154 <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." />
155 155
156 <conditional name="correction_select"> 156 <conditional name="correction_select">
157 <param name="correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'" > 157 <param name="correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'" >
158 <option value="no_corr">No correction</option> 158 <option value="no_corr">No correction</option>
159 <option value="p_value">p_value</option> 159 <option value="p_value">p_value</option>
172 </when> 172 </when>
173 </conditional> 173 </conditional>
174 174
175 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" /> 175 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />
176 176
177 <param name="write_single_snp" argument="--write_single_snp" truevalue="--write_single_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to only the first SNP per locus." /> 177 <param argument="--write_single_snp" truevalue="--write_single_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to only the first SNP per locus." />
178 <param name="write_random_snp" argument="--write_random_snp" truevalue="--write_random_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to one random SNP per locus." /> 178 <param argument="--write_random_snp" truevalue="--write_random_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to one random SNP per locus." />
179 </section> 179 </section>
180 180
181 <section name="populations_output" title="Output options" expanded="true"> 181 <section name="populations_output" title="Output options" expanded="true">
182 <param name="ordered_export" 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." /> 182 <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." />
183 <param name="vcf" argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" /> 183 <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" />
184 <param name="vcf_haplotypes" argument="--vcf_haplotypes" truevalue="--vcf_haplotypes" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Variant Call Format (VCF)." /> 184 <param argument="--vcf_haplotypes" truevalue="--vcf_haplotypes" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Variant Call Format (VCF)." />
185 <param name="genepop" argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" /> 185 <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" />
186 <param name="structure" argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" /> 186 <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" />
187 <param name="fasta" argument="--fasta" truevalue="--fasta" falsevalue="" type="boolean" checked="false" label="Output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility." /> 187 <param argument="--fasta" truevalue="--fasta" falsevalue="" type="boolean" checked="false" label="Output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility." />
188 <param name="fasta_strict" argument="--fasta_strict" truevalue="--fasta_strict" falsevalue="" type="boolean" checked="false" label="Output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci." /> 188 <param argument="--fasta_strict" truevalue="--fasta_strict" falsevalue="" type="boolean" checked="false" label="Output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci." />
189 <param name="hzar" argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." /> 189 <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." />
190 <param name="phase" argument="--phase" truevalue="--phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" /> 190 <param argument="--phase" truevalue="--phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" />
191 <param name="fastphase" argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" /> 191 <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" />
192 <param name="beagle" argument="--beagle" truevalue="--beagle" falsevalue="" type="boolean" checked="false" label="Output genotypes in Beagle format" /> 192 <param argument="--beagle" truevalue="--beagle" falsevalue="" type="boolean" checked="false" label="Output genotypes in Beagle format" />
193 <param name="beagle_phased" argument="--beagle_phased" truevalue="--beagle_phased" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Beagle format" /> 193 <param argument="--beagle_phased" truevalue="--beagle_phased" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Beagle format" />
194 <param name="plink" argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" /> 194 <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" />
195 <param name="phylip" 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" /> 195 <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" />
196 <param name="phylip_var" argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." /> 196 <param argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." />
197 <param name="phylip_var_all" 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." /> 197 <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." />
198 <param name="treemix" argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)." /> 198 <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)." />
199 199
200 <conditional name="options_genomic"> 200 <conditional name="options_genomic">
201 <param name="genomic" argument="--genomic" truevalue="--genomic" falsevalue="" type="boolean" checked="false" label="Output each nucleotide position (fixed or polymorphic) in all population members to a file" /> 201 <param argument="--genomic" type="select" checked="false" label="Output each nucleotide position (fixed or polymorphic) in all population members to a file">
202 <option value="--genomic">Yes</option>
203 <option value="">No</option>
204 </param>
202 <when value="--genomic"> 205 <when value="--genomic">
203 <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" > 206 <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" >
204 <expand macro="enzymes"/> 207 <expand macro="enzymes"/>
205 </param> 208 </param>
206 </when> 209 </when>
207 <when value=""> 210 <when value=""/>
208 </when>
209 </conditional> 211 </conditional>
210 </section> 212 </section>
211 213
212 <param name="fstats" argument="--fstats" truevalue="--fstats" falsevalue="" type="boolean" checked="false" label="Enable SNP and haplotype-based F statistics" /> 214 <param argument="--fstats" truevalue="--fstats" falsevalue="" type="boolean" checked="false" label="Enable SNP and haplotype-based F statistics" />
213 215
214 <conditional name="options_kernel"> 216 <conditional name="options_kernel">
215 <param name="kernel" type="boolean" checked="false" truevalue="-k" falsevalue="" label="enable kernel-smoothed FIS, π, and FST calculations" /> 217 <param name="kernel" type="select" checked="false" label="enable kernel-smoothed FIS, π, and FST calculations">
218 <option value="-k">Yes</option>
219 <option value="" selected="true">No</option>
220 </param>
216 <when value="-k"> 221 <when value="-k">
217 <param name="sigma" type="integer" value="150" label="Sigma" help="Standard deviation of the kernel smoothing weight distribution (sigma, default 150Kb)" /> 222 <param name="sigma" type="integer" value="150" label="Sigma" help="Standard deviation of the kernel smoothing weight distribution (sigma, default 150Kb)" />
218 </when> 223 </when>
219 <when value=""> 224 <when value=""/>
220 </when>
221 </conditional> 225 </conditional>
222 226
223 <section name="bootstrap_resampling" title="Bootstrap resampling" expanded="false"> 227 <section name="bootstrap_resampling" title="Bootstrap resampling" expanded="false">
224 <conditional name="bootstrap_resampling_mode"> 228 <conditional name="bootstrap_resampling_mode">
225 <param name="bootstrap_all" argument="--bootstrap" type="boolean" checked="false" truevalue="--bootstrap" falsevalue="" label="Enable bootstrap resampling for all smoothed statistics" /> 229 <param name="bootstrap_all" argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics">
226 <when value="--bootstrap"> 230 <option value="--bootstrap">Yes</option>
227 </when> 231 <option value="" selected="true">No</option>
232 </param>
233 <when value="--bootstrap"/>
228 <when value=""> 234 <when value="">
229 <param name="bootstrap_pifis" argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" /> 235 <param argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" />
230 <param name="bootstrap_fst" 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" /> 236 <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" />
231 <param name="bootstrap_div" 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" /> 237 <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" />
232 <param name="bootstrap_phist" argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." /> 238 <param argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." />
233 </when> 239 </when>
234 </conditional> 240 </conditional>
235 <param name="bootstrap_reps" argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" /> 241 <param argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" />
236 <param name="bootstrap_wl" argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" /> 242 <param argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" />
237 </section> 243 </section>
238 244
239 <!-- Output options --> 245 <!-- Output options -->
240 <section name="advanced_options" title="advanced options" expanded="False"> 246 <section name="advanced_options" title="advanced options" expanded="False">
241 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing Whitelisted markers to include in the export" /> 247 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing Whitelisted markers to include in the export" />