Mercurial > repos > iuc > stacks2_populations
diff stacks_populations.xml @ 4:887cf585cafc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author | iuc |
---|---|
date | Tue, 27 Apr 2021 09:38:08 +0000 |
parents | b242deb58952 |
children | e2db212d64ad |
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--- a/stacks_populations.xml Thu Jul 16 07:32:42 2020 -0400 +++ b/stacks_populations.xml Tue Apr 27 09:38:08 2021 +0000 @@ -129,6 +129,7 @@ $populations_output.treemix $populations_output.no_hap_exports $populations_output.fasta_samples_raw +$populations_output.gtf #if $genetic_map_options.map_type: --map-type $genetic_map_options.map_type @@ -244,14 +245,15 @@ <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="--gtf" truevalue="--gtf" falsevalue="" type="boolean" checked="false" label="output locus positions in a GTF annotation file"/> </section> <!-- Kernel-smoothing algorithm --> <section name="kernel_smoothing" title="Kernel smoothing" expanded="false"> <conditional name="options_kernel"> - <param name="kernel" type="select" label="Enable kernel-smoothed calculations" > + <param name="kernel" type="select" label="Enable kernel-smoothed calculations" help="The options -k and --smooth-fstats implicitly enable --fstats. Note that, in order to set non-default values for --fst-correction or --p-value-cutoff the option --fstats still needs to be enabled in the tool form." > <option value="">No</option> - <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</option> + <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k/--smooth)</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> @@ -348,7 +350,7 @@ <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 expect_num_outputs="26"> + <test expect_num_outputs="27"> <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> @@ -372,6 +374,7 @@ <param name="populations_output|structure" value="yes"/> <param name="populations_output|radpainter" value="yes"/> <param name="populations_output|treemix" value="yes"/> + <param name="populations_output|gtf" value="yes"/> <assert_command> <has_text text="--log-fst-comp"/> </assert_command> @@ -402,6 +405,7 @@ <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " --> <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " --> <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " --> + <output ftype="gtf" name="out_gtf" value="populations/populations.gtf" lines_diff="2"/><!-- " --> </test> <!-- test w vcf input and default options, just checking if finished --> <test expect_num_outputs="6"> @@ -526,7 +530,7 @@ <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 expect_num_outputs="6"> + <test expect_num_outputs="9"> <param name="options_usage|input_type" value="stacks"/> <param name="options_usage|input_aln"> <collection type="list"> @@ -564,8 +568,54 @@ <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_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"/> </test> - <!-- test w gstacks output as input and default options --> + <!-- same as previous test but without fstats parameter in order to check if the filter + for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats + is used) --> + <test expect_num_outputs="9"> + <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"/> + </collection> + </param> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <conditional name="fstats_conditional"> + <param name="fstats" value="no"/> + </conditional> + <conditional name="options_kernel"> + <param name="kernel" value="--smooth-fstats"/> + <param name="sigma" value="150001"/> + </conditional> + <conditional name="bootstrap_resampling_mode"> + <param name="bootstrap" value="--bootstrap"/> + </conditional> + <param name="bootstrap_reps" value="23"/> + <param name="add_log" value="yes"/> + <assert_command> + <not_has_text text="--fstats"/> + <not_has_text text="--fst-correction"/> + <not_has_text text="--p-value-cutoff 0.01"/> + <has_text text="--smooth-fstats "/> + <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="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_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"/> + </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">