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comparison stacks_populations.xml @ 4:887cf585cafc draft

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"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
comparison
equal deleted inserted replaced
3:b242deb58952 4:887cf585cafc
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"/>