Mercurial > repos > iuc > stacks2_populations
diff stacks_populations.xml @ 3:b242deb58952 draft
"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 |
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--- a/stacks_populations.xml Wed Feb 12 18:22:03 2020 -0500 +++ b/stacks_populations.xml Thu Jul 16 07:32:42 2020 -0400 @@ -51,14 +51,14 @@ --min-samples-per-pop $options_filtering.minperc --min-samples-overall $options_filtering.min_samples_overall $options_filtering.filter_haplotype_wise ---min_maf $options_filtering.min_maf ---min_mac $options_filtering.min_mac +--min-maf $options_filtering.min_maf +--min-mac $options_filtering.min_mac #if str($options_filtering.max_obs_het) - --max_obs_het $options_filtering.max_obs_het + --max-obs-het $options_filtering.max_obs_het #end if ## deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ ## #if str($options_filtering.lnl) -## --lnl_lim $options_filtering.lnl +## --lnl-lim $options_filtering.lnl ## #end if $options_filtering.filter_single_snp #if $options_filtering.blacklist @@ -73,7 +73,7 @@ -e $merge_phase.enzyme #end if $merge_phase.merge_sites ---merge_prune_lim $merge_phase.merge_prune_lim +--merge-prune-lim $merge_phase.merge_prune_lim ## Locus stats: $locus_stats.hwe @@ -81,9 +81,9 @@ ## Fstats #if str($fstats_conditional.fstats) != 'no': --fstats - #if str( $fstats_conditional.correction_select.fst_correction ) != "no_corr" - --fst_correction $fstats_conditional.correction_select.fst_correction - --p_value_cutoff $fstats_conditional.correction_select.p_value_cutoff + $fstats_conditional.fst_correction + #if $fstats_conditional.fst_correction + --p-value-cutoff $fstats_conditional.p_value_cutoff #end if #end if @@ -103,10 +103,10 @@ #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 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist: #if str($kernel_smoothing.bootstrap_reps) - --bootstrap_reps $kernel_smoothing.bootstrap_reps + --bootstrap-reps $kernel_smoothing.bootstrap_reps #end if #if $kernel_smoothing.bootstrap_wl - --bootstrap_wl '$kernel_smoothing.bootstrap_wl' + --bootstrap-wl '$kernel_smoothing.bootstrap_wl' #end if #end if @@ -130,6 +130,13 @@ $populations_output.no_hap_exports $populations_output.fasta_samples_raw +#if $genetic_map_options.map_type: + --map-type $genetic_map_options.map_type +#end if +#if $genetic_map_options.map_format + --map-format $genetic_map_options.map_format +#end if + ## Additional options: $advanced_options.log_fst_comp @@ -146,6 +153,12 @@ #end if && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done #end if + +## move the genotype output (note that in 2.52 there is an inconsistent +## naming for onemap output and also extensions are inconsistent -> therefore wildcard) +#if $genetic_map_options.map_type and $genetic_map_options.map_format + && mv stacks_outputs/populations.${genetic_map_options.map_type}.* stacks_outputs/populations.sql.tsv +#end if ]]></command> <inputs> @@ -158,31 +171,31 @@ <expand macro="input_aln_macro"/> </when> <when value="vcf"> - <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" /> + <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V"/> </when> </conditional> <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"/> - <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)"/> + <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)"/> <!-- Data Filtering --> <section name="options_filtering" title="Data filtering options" expanded="true"> - <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" /> - <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" /> - <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" /> - <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." /> - <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" /> - <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" /> - <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." /> + <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"/> + <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"/> + <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"/> + <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."/> + <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"/> + <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"/> + <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."/> <!-- deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ - <param type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold" />--> + <param type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold"/>--> <param name="filter_single_snp" type="select" label="Analyse all SNPs per locus" > <option value="">yes</option> - <option value="--write_single_snp">No: Analyse only the first SNP (--write_single_snp)</option> - <option value="--write_random_snp">No: Analyse only one random SNP (--write_random_snp)</option> + <option value="--write-single-snp">No: Analyse only the first SNP (--write-single-snp)</option> + <option value="--write-random-snp">No: Analyse only one random SNP (--write-random-snp)</option> </param> - <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export" /> - <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export" /> + <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export"/> + <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export"/> </section> <!-- merging and Phasing --> @@ -190,13 +203,13 @@ <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" > <expand macro="enzymes"/> </param> - <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)" /> - <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"/> + <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)"/> + <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"/> </section> <!-- Locus stats --> <section name="locus_stats" title="Locus Stats" expanded="true"> - <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="Calculate divergence from Hardy-Weinberg equilibrium for each locus" /> + <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="Calculate divergence from Hardy-Weinberg equilibrium for each locus"/> </section> <!-- Fstats --> @@ -207,46 +220,30 @@ </param> <when value="no"/> <when value="yes"> - <conditional name="correction_select"> - <param argument="--fst_correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values" > - <option value="no_corr">No correction</option> - <option value="p_value">p_value</option> - <option value="bonferroni_win">bonferroni_win</option> - <option value="bonferroni_gen">bonferroni_gen</option> - </param> - <when value="no_corr"/> - <when value="p_value"> - <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" /> - </when> - <when value="bonferroni_win"> - <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" /> - </when> - <when value="bonferroni_gen"> - <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" /> - </when> - </conditional> + <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=""/> + <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)."/> </when> </conditional> <!-- File output options --> <section name="populations_output" title="Output options" expanded="true"> - <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." /> - <param argument="--fasta_loci" truevalue="--fasta_loci" falsevalue="" type="boolean" checked="false" label="Output locus consensus sequences in FASTA format" /> - <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" /> - <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" /> - <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" /> - <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" /> - <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format" /> - <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" />--> - <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" /> - <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" /> - <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." /> - <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" /> - <param argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." /> - <!--<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." />--> - <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)." /> - <param argument="--no_hap_exports" truevalue="--no_hap_exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs" /> - <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" /> + <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."/> + <param argument="--fasta-loci" truevalue="--fasta-loci" falsevalue="" type="boolean" checked="false" label="Output locus consensus sequences in FASTA format"/> + <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"/> + <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/> + <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/> + <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/> + <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/> + <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format"/>--> + <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format"/> + <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/> + <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/> + <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"/> + <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/> + <!--<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."/>--> + <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)."/> + <param argument="--no-hap-exports" truevalue="--no-hap-exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs"/> + <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"/> </section> <!-- Kernel-smoothing algorithm --> @@ -255,18 +252,18 @@ <param name="kernel" type="select" label="Enable kernel-smoothed calculations" > <option value="">No</option> <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</option> - <option value="--smooth_fstats">For Fst, Fst', and Phi_st (--smooth_fstats)</option> - <option value="--smooth_popstats">For Pi and Fis (--smooth_popstats)</option> + <option value="--smooth-fstats">For Fst, Fst', and Phi_st (--smooth-fstats)</option> + <option value="--smooth-popstats">For Pi and Fis (--smooth-popstats)</option> </param> <when value=""/> <when value="-k"> - <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)" /> + <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)"/> </when> - <when value="--smooth_fstats"> - <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)" /> + <when value="--smooth-fstats"> + <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)"/> </when> - <when value="--smooth_popstats"> - <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)" /> + <when value="--smooth-popstats"> + <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)"/> </when> </conditional> <conditional name="bootstrap_resampling_mode"> @@ -277,19 +274,34 @@ <when value="--bootstrap"> </when> <when value=""> - <param argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" /> - <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" /> - <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" /> - <param argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." /> + <param argument="--bootstrap-pifis" type="boolean" checked="false" truevalue="--bootstrap-pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations"/> + <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"/> + <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"/> + <param argument="--bootstrap-phist" type="boolean" checked="false" truevalue="--bootstrap-phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes."/> </when> </conditional> - <param argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" /> - <param argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" /> + <param argument="--bootstrap-reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate"/> + <param argument="--bootstrap-wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist"/> </section> <!-- Output options --> <section name="advanced_options" title="Advanced options" expanded="False"> - <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" /> + <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"/> + </section> + + <!-- Genetic map output options (population map must specify a genetic cross): --> + <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"> + <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"> + <option value="CP">CP</option> + <option value="DH">DH</option> + <option value="F2">F2</option> + <option value="BC1">BC1</option> + </param> + <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"> + <option value="joinmap">joinmap</option> + <option value="onemap">onemap</option> + <option value="rqtl">rqtl</option> + </param> </section> <expand macro="in_log"/> </inputs> @@ -297,57 +309,55 @@ <expand macro="out_log"/> <expand macro="populations_output_full"/> </outputs> - <tests> <!-- test w gstacks output as input and default options --> - <test> - <param name="options_usage|input_type" value="stacks" /> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> - <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> - <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="batch_size" value="9999" /> - <param name="add_log" value="yes" /> + <param name="batch_size" value="9999"/> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="batch_size" value="9999"/> + <param name="add_log" value="yes"/> <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/> <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/> <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> - <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/> </test> <!-- test w gstacks output as input, wo popmap, and default options --> - <test> - <param name="options_usage|input_type" value="stacks" /> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> - <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> - <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> </collection> </param> - <param name="add_log" value="yes" /> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> - <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output> + <param name="add_log" value="yes"/> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> + <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> </test> <!-- test w gstacks output as input and + all outputs --> - <test> - <param name="options_usage|input_type" value="stacks" /> + <test expect_num_outputs="26"> + <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> - <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> - <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="add_log" value="yes" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="add_log" value="yes"/> <param name="advanced_options|log_fst_comp" value="yes"/> <param name="fstats_conditional|fstats" value="yes"/> <param name="populations_output|fasta_loci" value="yes"/> @@ -363,21 +373,20 @@ <param name="populations_output|radpainter" value="yes"/> <param name="populations_output|treemix" value="yes"/> <assert_command> - <has_text text="--log_fst_comp" /> + <has_text text="--log-fst-comp"/> </assert_command> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/> <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> - <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/> <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> - <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 --> - <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " --> + <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 --> + <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " --> <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " --> <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/><!-- " --> <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/> @@ -395,175 +404,207 @@ <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " --> </test> <!-- test w vcf input and default options, just checking if finished --> - <test> - <param name="options_usage|input_type" value="vcf" /> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="vcf"/> <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="add_log" value="yes" /> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> - <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="add_log" value="yes"/> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> + <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> </test> <!-- test w gstacks output as input and non default filtering --> - <test> - <param name="options_usage|input_type" value="stacks" /> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> - <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> - <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="add_log" value="yes" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="add_log" value="yes"/> <section name="options_filtering"> <param name="minperc" value="0.1"/> <param name="minpop" value="2"/> <param name="min_samples_overall" value="0.01"/> <param name="filter_haplotype_wise" value="--filter-haplotype-wise"/> - <param name="min_maf" value="0.01" /> + <param name="min_maf" value="0.01"/> <param name="min_mac" value="1"/> - <param name="max_obs_het" value="0.8" /> - <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> + <param name="max_obs_het" value="0.8"/> + <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/> </section> <assert_command> - <has_text text="--min-samples-per-pop 0.1" /> - <has_text text="--min-populations 2" /> - <has_text text="--min-samples-overall 0.01" /> - <has_text text="--filter-haplotype-wise" /> - <has_text text="--min_maf 0.01" /> - <has_text text="--min_mac 1" /> - <has_text text="--max_obs_het 0.8" /> - <has_text text="-B " /> + <has_text text="--min-samples-per-pop 0.1"/> + <has_text text="--min-populations 2"/> + <has_text text="--min-samples-overall 0.01"/> + <has_text text="--filter-haplotype-wise"/> + <has_text text="--min-maf 0.01"/> + <has_text text="--min-mac 1"/> + <has_text text="--max-obs-het 0.8"/> + <has_text text="-B "/> </assert_command> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> - <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> + <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> </test> <!-- test w gstacks output as input and non default filtering (needed because filter-haplotype-wise is incompatible with write_random_snp/write_single_snp) --> - <test> - <param name="options_usage|input_type" value="stacks" /> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> - <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> - <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="add_log" value="yes" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="add_log" value="yes"/> <section name="options_filtering"> <param name="minperc" value="0.1"/> <param name="minpop" value="2"/> <param name="min_samples_overall" value="0.01"/> - <param name="min_maf" value="0.01" /> + <param name="min_maf" value="0.01"/> <param name="min_mac" value="1"/> - <param name="max_obs_het" value="0.8" /> + <param name="max_obs_het" value="0.8"/> <!-- since write_random_snp runs in infinite loop switch to write_single --> - <param name="filter_single_snp" value="--write_single_snp"/> - <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> + <param name="filter_single_snp" value="--write-single-snp"/> + <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/> </section> <assert_command> - <has_text text="--min-samples-per-pop 0.1" /> - <has_text text="--min-populations 2" /> - <has_text text="--min-samples-overall 0.01" /> - <has_text text="--min_maf 0.01" /> - <has_text text="--min_mac 1" /> - <has_text text="--max_obs_het 0.8" /> - <not_has_text text="--write_random_snp" /> - <has_text text="-B " /> + <has_text text="--min-samples-per-pop 0.1"/> + <has_text text="--min-populations 2"/> + <has_text text="--min-samples-overall 0.01"/> + <has_text text="--min-maf 0.01"/> + <has_text text="--min-mac 1"/> + <has_text text="--max-obs-het 0.8"/> + <not_has_text text="--write-random-snp"/> + <has_text text="-B "/> </assert_command> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> - <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> + <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> </test> <!-- test w gstacks output as input and non default merging/hwe --> - <test> - <param name="options_usage|input_type" value="stacks" /> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> - <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> - <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> <section name="merge_phase"> <param name="enzyme" value="ecoRI"/> <param name="merge_sites" value="yes"/> - <param name="merge_prune_lim" value="0.9" /> + <param name="merge_prune_lim" value="0.9"/> </section> <section name="locus_stats"> - <param name="hwe" value="yes" /> + <param name="hwe" value="yes"/> </section> - <param name="add_log" value="yes" /> + <param name="add_log" value="yes"/> <assert_command> - <has_text text="-e ecoRI" /> - <has_text text="--merge_sites" /> - <has_text text="--merge_prune_lim 0.9" /> - <has_text text="--hwe" /> + <has_text text="-e ecoRI"/> + <has_text text="--merge-sites"/> + <has_text text="--merge-prune-lim 0.9"/> + <has_text text="--hwe"/> </assert_command> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> - <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> + <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> </test> <!-- test w gstacks output as input and non default fstats/kernel/bootstrap --> - <test> - <param name="options_usage|input_type" value="stacks" /> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> - <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf" /> - <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz" /> + <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> <conditional name="fstats_conditional"> - <param name="fstats" value="yes" /> - <conditional name="correction_select"> - <param name="fst_correction" value="bonferroni_gen"/> - <param name="p_value_cutoff" value="0.01" /> - </conditional> + <param name="fstats" value="yes"/> + <param name="fst_correction" value="--fst-correction"/> + <param name="p_value_cutoff" value="0.01"/> </conditional> <conditional name="options_kernel"> - <param name="kernel" value="-k" /> - <param name="sigma" value="150001" /> + <param name="kernel" value="-k"/> + <param name="sigma" value="150001"/> </conditional> <conditional name="bootstrap_resampling_mode"> - <param name="bootstrap" value="--bootstrap" /> + <param name="bootstrap" value="--bootstrap"/> </conditional> - <param name="bootstrap_reps" value="23" /> - <param name="add_log" value="yes" /> + <param name="bootstrap_reps" value="23"/> + <param name="add_log" value="yes"/> <assert_command> - <has_text text="--fstats" /> - <has_text text="--fst_correction bonferroni_gen" /> - <has_text text="--p_value_cutoff 0.01" /> - <has_text text="-k " /> - <has_text text="--sigma 150001" /> - <has_text text="--bootstrap" /> - <has_text text="--bootstrap_reps 23" /> + <has_text text="--fstats"/> + <has_text text="--fst-correction"/> + <has_text text="--p-value-cutoff 0.01"/> + <has_text text="-k "/> + <has_text text="--sigma 150001"/> + <has_text text="--bootstrap"/> + <has_text text="--bootstrap-reps 23"/> </assert_command> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> - <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> - <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="" /></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="" /></assert_contents></output> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> + <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> + </test> + <!-- test w gstacks output as input and default options --> + <test expect_num_outputs="6"> + <param name="options_usage|input_type" value="stacks"/> + <param name="options_usage|input_aln"> + <collection type="list"> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> + </collection> + </param> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="add_log" value="yes"/> + <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/> + <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> + <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> + <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/> + <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> + <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> + </test> + <!-- test w gstacks output as input, wo popmap, and Genetic map output options that have been added in 2.5 --> + <test expect_num_outputs="7"> + <param name="options_usage|input_type" value="stacks"/> + <param name="options_usage|input_aln"> + <collection type="list"> + <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> + <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> + </collection> + </param> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks_genotypes.tsv"/> + <section name="genetic_map_options"> + <param name="map_type" value="CP"/> + <param name="map_format" value="joinmap"/> + </section> + <param name="add_log" value="yes"/> + <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> + <output ftype="txt" name="out_sql" file="populations/populations.CP.joinmap.loc" lines_diff="4"/> + <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> + <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> </test> </tests> <help> @@ -625,5 +666,5 @@ @STACKS_INFOS@ ]]> </help> - <expand macro="citation" /> + <expand macro="citation"/> </tool>