| Previous changeset 11:95286af4139b (2022-03-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb |
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modified:
macros.xml stacks_populations.xml |
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| diff -r 95286af4139b -r d1fad35bdb4a macros.xml --- a/macros.xml Tue Mar 22 23:19:46 2022 +0000 +++ b/macros.xml Fri Apr 07 22:00:26 2023 +0000 |
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| @@ -343,7 +343,7 @@ <option value="fixed">Fixed</option> </param> <when value="snp"> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -351,9 +351,9 @@ </param> </when> <when value="bounded"> - <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> - <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> + <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -373,7 +373,7 @@ <option value="fixed">Fixed</option> </param> <when value="snp"> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -381,9 +381,9 @@ </param> </when> <when value="bounded"> - <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> - <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> + <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -391,7 +391,7 @@ </param> </when> <when value="fixed"> - <param name="bc_err_freq" argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> + <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> </when> </conditional> </xml> |
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| diff -r 95286af4139b -r d1fad35bdb4a stacks_populations.xml --- a/stacks_populations.xml Tue Mar 22 23:19:46 2022 +0000 +++ b/stacks_populations.xml Fri Apr 07 22:00:26 2023 +0000 |
| [ |
| b'@@ -1,9 +1,9 @@\n-<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.2">\n+<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.3">\n <description>analyze a population of individual samples (\'populations\' program)</description>\n- <expand macro="bio_tools"/>\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <expand macro="bio_tools"/>\n <expand macro="requirements"/>\n <expand macro="stdio"/>\n <command><![CDATA[\n@@ -20,11 +20,11 @@\n #set $filename = $filename + ".tsv"\n #end if\n #if re.search(\'\\.(tags|snps|alleles|matches)(\\.tsv)?$\', $filename)\n- ln -s \'${input_file}\' \'stacks_outputs/${filename}\' &&\n+ cp \'${input_file}\' \'stacks_outputs/${filename}\' &&\n #end if\n #end for\n #else if str($options_usage.input_type) == \'vcf\'\n- ln -s \'$options_usage.input_vcf\' \'stacks_outputs/batch_1.vcf\' &&\n+ cp \'$options_usage.input_vcf\' \'stacks_outputs/batch_1.vcf\' &&\n #end if\n \n populations\n@@ -66,13 +66,13 @@\n ## Fstats\n $fstats\n \n- #if $options_kernel.kernel\n+ #if $options_kernel.kernel != ""\n -k\n --sigma $options_kernel.sigma\n #end if\n \n ## Bootstrap resampling options\n- #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all\n+ #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all != ""\n --bootstrap\n #else\n $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_pifis\n@@ -107,7 +107,7 @@\n $populations_output.phylip_var_all\n $populations_output.treemix\n \n- #if $populations_output.options_genomic.genomic\n+ #if $populations_output.options_genomic.genomic != \'\'\n --genomic\n -e $populations_output.options_genomic.enzyme\n #end if\n@@ -151,7 +151,7 @@\n <param name="minpop" argument="-p" type="integer" value="2" label="Minimum number of populations a locus must be present in to process a locus" />\n <param name="mindepth" argument="-m" type="integer" value="1" label="Specify a minimum stack depth required for individuals at a locus" />\n <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)" />\n- <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." />\n+ <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." />\n \n <conditional name="correction_select">\n <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\'" >\n@@ -174,66 +174,72 @@\n \n <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />\n \n- <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." />\n- <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." />\n+ <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." />\n+ <param'..b'T calculations">\n+ <option value="-k">Yes</option>\n+ <option value="" selected="true">No</option>\n+ </param>\n <when value="-k">\n <param name="sigma" type="integer" value="150" label="Sigma" help="Standard deviation of the kernel smoothing weight distribution (sigma, default 150Kb)" />\n </when>\n- <when value="">\n- </when>\n+ <when value=""/>\n </conditional>\n \n <section name="bootstrap_resampling" title="Bootstrap resampling" expanded="false">\n <conditional name="bootstrap_resampling_mode">\n- <param name="bootstrap_all" argument="--bootstrap" type="boolean" checked="false" truevalue="--bootstrap" falsevalue="" label="Enable bootstrap resampling for all smoothed statistics" />\n- <when value="--bootstrap">\n- </when>\n+ <param name="bootstrap_all" argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics">\n+ <option value="--bootstrap">Yes</option>\n+ <option value="" selected="true">No</option>\n+ </param>\n+ <when value="--bootstrap"/>\n <when value="">\n- <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" />\n- <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" />\n- <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" />\n- <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." />\n+ <param argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" />\n+ <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" />\n+ <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" />\n+ <param argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." />\n </when>\n </conditional>\n- <param name="bootstrap_reps" argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" />\n- <param name="bootstrap_wl" argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" />\n+ <param argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" />\n+ <param argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" />\n </section>\n \n <!-- Output options -->\n' |