Mercurial > repos > iuc > stacks2_populations
comparison stacks_populations.xml @ 8:564c33e5c3e3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
| author | iuc |
|---|---|
| date | Mon, 23 May 2022 17:47:23 +0000 |
| parents | e2db212d64ad |
| children |
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| 7:a5969aa9347e | 8:564c33e5c3e3 |
|---|---|
| 344 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> | 344 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> |
| 345 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> | 345 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> |
| 346 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> | 346 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> |
| 347 </test> | 347 </test> |
| 348 <!-- test w gstacks output as input and + all outputs --> | 348 <!-- test w gstacks output as input and + all outputs --> |
| 349 <test expect_num_outputs="27"> | 349 <test expect_num_outputs="28"> |
| 350 <param name="options_usage|input_type" value="stacks"/> | 350 <param name="options_usage|input_type" value="stacks"/> |
| 351 <param name="options_usage|input_aln"> | 351 <param name="options_usage|input_aln"> |
| 352 <collection type="list"> | 352 <collection type="list"> |
| 353 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> | 353 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/> |
| 354 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> | 354 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/> |
| 375 <has_text text="--log-fst-comp"/> | 375 <has_text text="--log-fst-comp"/> |
| 376 </assert_command> | 376 </assert_command> |
| 377 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> | 377 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output> |
| 378 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> | 378 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> |
| 379 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> | 379 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> |
| 380 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/> | 380 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"> |
| 381 <assert_contents> | |
| 382 <has_text text="Calculating F statistics...done."/> | |
| 383 </assert_contents> | |
| 384 </output> | |
| 381 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> | 385 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> |
| 382 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> | 386 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> |
| 383 | 387 |
| 384 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> | 388 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> |
| 385 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> | 389 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> |
| 386 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> | 390 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> |
| 391 <output_collection name="out_fstats_popcompare" type="list" count="0"/> | |
| 387 <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 --> | 392 <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 --> |
| 388 <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " --> | 393 <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " --> |
| 389 <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " --> | 394 <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " --> |
| 390 <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/><!-- " --> | 395 <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/><!-- " --> |
| 391 <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/> | 396 <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/> |
| 524 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output> | 529 <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> | 530 <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> | 531 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> |
| 527 </test> | 532 </test> |
| 528 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap --> | 533 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap --> |
| 529 <test expect_num_outputs="9"> | 534 <test expect_num_outputs="10"> |
| 530 <param name="options_usage|input_type" value="stacks"/> | 535 <param name="options_usage|input_type" value="stacks"/> |
| 531 <param name="options_usage|input_aln"> | 536 <param name="options_usage|input_aln"> |
| 532 <collection type="list"> | 537 <collection type="list"> |
| 533 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/> | 538 <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"/> | 539 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/> |
| 535 </collection> | 540 </collection> |
| 536 </param> | 541 </param> |
| 537 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> | 542 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks_genotypes.tsv"/> |
| 538 <conditional name="fstats_conditional"> | 543 <conditional name="fstats_conditional"> |
| 539 <param name="fstats" value="yes"/> | 544 <param name="fstats" value="yes"/> |
| 540 <param name="fst_correction" value="--fst-correction"/> | 545 <param name="fst_correction" value="--fst-correction"/> |
| 541 <param name="p_value_cutoff" value="0.01"/> | 546 <param name="p_value_cutoff" value="0.01"/> |
| 542 </conditional> | 547 </conditional> |
| 563 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output> | 568 <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> | 569 <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> | 570 <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> | 571 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> |
| 567 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> | 572 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> |
| 568 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> | 573 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary_wgenotypes.tsv"/> |
| 569 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> | 574 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary_wgenotypes.tsv"/> |
| 575 <output_collection name="out_fstats_popcompare" type="list" count="1"> | |
| 576 <element name="parent-progeny" file="populations/populations.fst_parent-progeny.tsv" ftype="tabular"/> | |
| 577 </output_collection> | |
| 570 </test> | 578 </test> |
| 571 <!-- same as previous test but without fstats parameter in order to check if the filter | 579 <!-- same as previous test but without fstats parameter in order to check if the filter |
| 572 for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats | 580 for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats |
| 573 is used) --> | 581 is used) --> |
| 574 <test expect_num_outputs="9"> | 582 <test expect_num_outputs="10"> |
| 575 <param name="options_usage|input_type" value="stacks"/> | 583 <param name="options_usage|input_type" value="stacks"/> |
| 576 <param name="options_usage|input_aln"> | 584 <param name="options_usage|input_aln"> |
| 577 <collection type="list"> | 585 <collection type="list"> |
| 578 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/> | 586 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/> |
| 579 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/> | 587 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/> |
| 608 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> | 616 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output> |
| 609 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> | 617 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output> |
| 610 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> | 618 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/> |
| 611 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> | 619 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/> |
| 612 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> | 620 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/> |
| 621 <output_collection name="out_fstats_popcompare" type="list" count="0"/> | |
| 613 </test> | 622 </test> |
| 614 <!-- test w gstacks output as input and default options --> | 623 <!-- test w gstacks output as input and default options --> |
| 615 <test expect_num_outputs="6"> | 624 <test expect_num_outputs="6"> |
| 616 <param name="options_usage|input_type" value="stacks"/> | 625 <param name="options_usage|input_type" value="stacks"/> |
| 617 <param name="options_usage|input_aln"> | 626 <param name="options_usage|input_aln"> |