Mercurial > repos > iuc > stacks2_populations
comparison stacks_populations.xml @ 4:887cf585cafc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author | iuc |
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date | Tue, 27 Apr 2021 09:38:08 +0000 |
parents | b242deb58952 |
children | e2db212d64ad |
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3:b242deb58952 | 4:887cf585cafc |
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127 $populations_output.phylip_var | 127 $populations_output.phylip_var |
128 ##$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 $populations_output.gtf | |
132 | 133 |
133 #if $genetic_map_options.map_type: | 134 #if $genetic_map_options.map_type: |
134 --map-type $genetic_map_options.map_type | 135 --map-type $genetic_map_options.map_type |
135 #end if | 136 #end if |
136 #if $genetic_map_options.map_format | 137 #if $genetic_map_options.map_format |
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."/> | 243 <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include 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."/>--> | 244 <!--<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."/>--> |
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)."/> | 245 <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)."/> |
245 <param argument="--no-hap-exports" truevalue="--no-hap-exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs"/> | 246 <param argument="--no-hap-exports" truevalue="--no-hap-exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs"/> |
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"/> | 247 <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"/> |
248 <param argument="--gtf" truevalue="--gtf" falsevalue="" type="boolean" checked="false" label="output locus positions in a GTF annotation file"/> | |
247 </section> | 249 </section> |
248 | 250 |
249 <!-- Kernel-smoothing algorithm --> | 251 <!-- Kernel-smoothing algorithm --> |
250 <section name="kernel_smoothing" title="Kernel smoothing" expanded="false"> | 252 <section name="kernel_smoothing" title="Kernel smoothing" expanded="false"> |
251 <conditional name="options_kernel"> | 253 <conditional name="options_kernel"> |
252 <param name="kernel" type="select" label="Enable kernel-smoothed calculations" > | 254 <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." > |
253 <option value="">No</option> | 255 <option value="">No</option> |
254 <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</option> | 256 <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k/--smooth)</option> |
255 <option value="--smooth-fstats">For Fst, Fst', and Phi_st (--smooth-fstats)</option> | 257 <option value="--smooth-fstats">For Fst, Fst', and Phi_st (--smooth-fstats)</option> |
256 <option value="--smooth-popstats">For Pi and Fis (--smooth-popstats)</option> | 258 <option value="--smooth-popstats">For Pi and Fis (--smooth-popstats)</option> |
257 </param> | 259 </param> |
258 <when value=""/> | 260 <when value=""/> |
259 <when value="-k"> | 261 <when value="-k"> |
346 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> | 348 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> |
347 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> | 349 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> |
348 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> | 350 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> |
349 </test> | 351 </test> |
350 <!-- test w gstacks output as input and + all outputs --> | 352 <!-- test w gstacks output as input and + all outputs --> |
351 <test expect_num_outputs="26"> | 353 <test expect_num_outputs="27"> |
352 <param name="options_usage|input_type" value="stacks"/> | 354 <param name="options_usage|input_type" value="stacks"/> |
353 <param name="options_usage|input_aln"> | 355 <param name="options_usage|input_aln"> |
354 <collection type="list"> | 356 <collection type="list"> |
355 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> | 357 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> |
356 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> | 358 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> |
370 <param name="populations_output|hzar" value="yes"/> | 372 <param name="populations_output|hzar" value="yes"/> |
371 <param name="populations_output|plink" value="yes"/> | 373 <param name="populations_output|plink" value="yes"/> |
372 <param name="populations_output|structure" value="yes"/> | 374 <param name="populations_output|structure" value="yes"/> |
373 <param name="populations_output|radpainter" value="yes"/> | 375 <param name="populations_output|radpainter" value="yes"/> |
374 <param name="populations_output|treemix" value="yes"/> | 376 <param name="populations_output|treemix" value="yes"/> |
377 <param name="populations_output|gtf" value="yes"/> | |
375 <assert_command> | 378 <assert_command> |
376 <has_text text="--log-fst-comp"/> | 379 <has_text text="--log-fst-comp"/> |
377 </assert_command> | 380 </assert_command> |
378 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> | 381 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> |
379 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> | 382 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> |
400 <output ftype="tabular" name="out_plink_genotypes" value="populations/populations.plink.ped" compare="sim_size" delta="50"/><!-- " --> | 403 <output ftype="tabular" name="out_plink_genotypes" value="populations/populations.plink.ped" compare="sim_size" delta="50"/><!-- " --> |
401 <output ftype="tabular" name="out_hzar" value="populations/populations.hzar.csv" compare="sim_size" delta="50"/><!-- " --> | 404 <output ftype="tabular" name="out_hzar" value="populations/populations.hzar.csv" compare="sim_size" delta="50"/><!-- " --> |
402 <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " --> | 405 <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " --> |
403 <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " --> | 406 <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " --> |
404 <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " --> | 407 <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " --> |
408 <output ftype="gtf" name="out_gtf" value="populations/populations.gtf" lines_diff="2"/><!-- " --> | |
405 </test> | 409 </test> |
406 <!-- test w vcf input and default options, just checking if finished --> | 410 <!-- test w vcf input and default options, just checking if finished --> |
407 <test expect_num_outputs="6"> | 411 <test expect_num_outputs="6"> |
408 <param name="options_usage|input_type" value="vcf"/> | 412 <param name="options_usage|input_type" value="vcf"/> |
409 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> | 413 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> |
524 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> | 528 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> |
525 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> | 529 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> |
526 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> | 530 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> |
527 </test> | 531 </test> |
528 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap --> | 532 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap --> |
529 <test expect_num_outputs="6"> | 533 <test expect_num_outputs="9"> |
530 <param name="options_usage|input_type" value="stacks"/> | 534 <param name="options_usage|input_type" value="stacks"/> |
531 <param name="options_usage|input_aln"> | 535 <param name="options_usage|input_aln"> |
532 <collection type="list"> | 536 <collection type="list"> |
533 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/> | 537 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/> |
534 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/> | 538 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/> |
562 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> | 566 <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> | 567 <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> | 568 <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> | 569 <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> | 570 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> |
567 </test> | 571 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> |
568 <!-- test w gstacks output as input and default options --> | 572 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> |
573 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> | |
574 </test> | |
575 <!-- same as previous test but without fstats parameter in order to check if the filter | |
576 for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats | |
577 is used) --> | |
578 <test expect_num_outputs="9"> | |
579 <param name="options_usage|input_type" value="stacks"/> | |
580 <param name="options_usage|input_aln"> | |
581 <collection type="list"> | |
582 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/> | |
583 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/> | |
584 </collection> | |
585 </param> | |
586 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> | |
587 <conditional name="fstats_conditional"> | |
588 <param name="fstats" value="no"/> | |
589 </conditional> | |
590 <conditional name="options_kernel"> | |
591 <param name="kernel" value="--smooth-fstats"/> | |
592 <param name="sigma" value="150001"/> | |
593 </conditional> | |
594 <conditional name="bootstrap_resampling_mode"> | |
595 <param name="bootstrap" value="--bootstrap"/> | |
596 </conditional> | |
597 <param name="bootstrap_reps" value="23"/> | |
598 <param name="add_log" value="yes"/> | |
599 <assert_command> | |
600 <not_has_text text="--fstats"/> | |
601 <not_has_text text="--fst-correction"/> | |
602 <not_has_text text="--p-value-cutoff 0.01"/> | |
603 <has_text text="--smooth-fstats "/> | |
604 <has_text text="--sigma 150001"/> | |
605 <has_text text="--bootstrap"/> | |
606 <has_text text="--bootstrap-reps 23"/> | |
607 </assert_command> | |
608 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> | |
609 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output> | |
610 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> | |
611 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> | |
612 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> | |
613 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> | |
614 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> | |
615 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> | |
616 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> | |
617 </test> | |
618 <!-- test w gstacks output as input and default options --> | |
569 <test expect_num_outputs="6"> | 619 <test expect_num_outputs="6"> |
570 <param name="options_usage|input_type" value="stacks"/> | 620 <param name="options_usage|input_type" value="stacks"/> |
571 <param name="options_usage|input_aln"> | 621 <param name="options_usage|input_aln"> |
572 <collection type="list"> | 622 <collection type="list"> |
573 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> | 623 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> |