Mercurial > repos > iuc > stacks2_gstacks
comparison macros.xml @ 3:eb784fa07f80 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
| author | iuc |
|---|---|
| date | Tue, 27 Apr 2021 09:31:18 +0000 |
| parents | 1d839ead7ad3 |
| children | 7370bb65bad4 |
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| 2:1d839ead7ad3 | 3:eb784fa07f80 |
|---|---|
| 7 <requirement type="package" version="4.6.0">findutils</requirement> | 7 <requirement type="package" version="4.6.0">findutils</requirement> |
| 8 <yield/> | 8 <yield/> |
| 9 </requirements> | 9 </requirements> |
| 10 </xml> | 10 </xml> |
| 11 | 11 |
| 12 <token name="@STACKS_VERSION@">2.53</token> | 12 <token name="@STACKS_VERSION@">2.55</token> |
| 13 <token name="@WRAPPER_VERSION@">0</token> | 13 <token name="@WRAPPER_VERSION@">0</token> |
| 14 <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 --> | 14 <token name="@PROFILE@">20.01</token> |
| 15 <token name="@PROFILE@">18.01</token> | |
| 16 | 15 |
| 17 <xml name="citation"> | 16 <xml name="citation"> |
| 18 <citations> | 17 <citations> |
| 19 <citation type="doi">10.1111/mec.12354</citation> | 18 <citation type="doi">10.1111/mec.12354</citation> |
| 20 <citation type="doi">10.1111/mec.12330</citation> | 19 <citation type="doi">10.1111/mec.12330</citation> |
| 65 <option value="bfuCI">bfuCI</option> | 64 <option value="bfuCI">bfuCI</option> |
| 66 <option value="bgIII">bgIII</option> | 65 <option value="bgIII">bgIII</option> |
| 67 <option value="bsaHI">bsaHI</option> | 66 <option value="bsaHI">bsaHI</option> |
| 68 <option value="bspDI">bspDI</option> | 67 <option value="bspDI">bspDI</option> |
| 69 <option value="bstYI">bstYI</option> | 68 <option value="bstYI">bstYI</option> |
| 69 <option value="btgI">btgI</option> | |
| 70 <option value="cac8I">cac8I</option> | 70 <option value="cac8I">cac8I</option> |
| 71 <option value="claI">claI</option> | 71 <option value="claI">claI</option> |
| 72 <option value="csp6I">csp6I</option> | 72 <option value="csp6I">csp6I</option> |
| 73 <option value="ddeI">ddeI</option> | 73 <option value="ddeI">ddeI</option> |
| 74 <option value="dpnII">dpnII</option> | 74 <option value="dpnII">dpnII</option> |
| 78 <option value="ecoT22I">ecoT22I</option> | 78 <option value="ecoT22I">ecoT22I</option> |
| 79 <option value="haeIII">haeIII</option> | 79 <option value="haeIII">haeIII</option> |
| 80 <option value="hindIII">hindIII</option> | 80 <option value="hindIII">hindIII</option> |
| 81 <option value="hinP1I">hinP1I</option> | 81 <option value="hinP1I">hinP1I</option> |
| 82 <option value="hpaII">hpaII</option> | 82 <option value="hpaII">hpaII</option> |
| 83 <option value="hpyCH4IV">hpyCH4IV</option> | |
| 83 <option value="kpnI">kpnI</option> | 84 <option value="kpnI">kpnI</option> |
| 84 <option value="mluCI">mluCI</option> | 85 <option value="mluCI">mluCI</option> |
| 85 <option value="mseI">mseI</option> | 86 <option value="mseI">mseI</option> |
| 86 <option value="mslI">mslI</option> | 87 <option value="mslI">mslI</option> |
| 87 <option value="mspI">mspI</option> | 88 <option value="mspI">mspI</option> |
| 88 <option value="ncoI">ncoI</option> | 89 <option value="ncoI">ncoI</option> |
| 89 <option value="ndeI">ndeI</option> | 90 <option value="ndeI">ndeI</option> |
| 90 <option value="nheI">nheI</option> | 91 <option value="nheI">nheI</option> |
| 92 <option value="ngoMIV">ngoMIV</option> | |
| 91 <option value="nlaIII">nlaIII</option> | 93 <option value="nlaIII">nlaIII</option> |
| 92 <option value="notI">notI</option> | 94 <option value="notI">notI</option> |
| 93 <option value="nsiI">nsiI</option> | 95 <option value="nsiI">nsiI</option> |
| 94 <option value="nspI">nspI</option> | 96 <option value="nspI">nspI</option> |
| 97 <option value="pacI">pacI</option> | |
| 98 <option value="pspXI">pspXI</option> | |
| 95 <option value="pstI">pstI</option> | 99 <option value="pstI">pstI</option> |
| 96 <option value="rsaI">rsaI</option> | 100 <option value="rsaI">rsaI</option> |
| 97 <option value="sacI">sacI</option> | 101 <option value="sacI">sacI</option> |
| 98 <option value="sau3AI">sau3AI</option> | 102 <option value="sau3AI">sau3AI</option> |
| 99 <option value="sbfI">sbfI</option> | 103 <option value="sbfI">sbfI</option> |
| 444 </xml> | 448 </xml> |
| 445 | 449 |
| 446 <xml name="populations_output_full"> | 450 <xml name="populations_output_full"> |
| 447 <expand macro="populations_output_light"/> | 451 <expand macro="populations_output_light"/> |
| 448 | 452 |
| 449 <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv"> | 453 <data format="txt" name="out_sql" label="${tool.name} on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv"> |
| 450 <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter> | 454 <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter> |
| 451 </data> | 455 </data> |
| 452 | 456 |
| 453 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> | 457 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> |
| 454 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> | 458 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> |
| 455 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> | 459 <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter> |
| 456 </data> | 460 </data> |
| 457 <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv"> | 461 <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv"> |
| 458 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> | 462 <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter> |
| 459 </data> | 463 </data> |
| 460 <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv"> | 464 <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv"> |
| 461 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> | 465 <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter> |
| 462 </data> | 466 </data> |
| 463 | 467 |
| 464 <!-- fasta_loci populations.loci.fa | 468 <!-- fasta_loci populations.loci.fa |
| 465 fasta_samples populations.samples.fa | 469 fasta_samples populations.samples.fa |
| 466 fasta_samples_raw populations.samples-raw.fa--> | 470 fasta_samples_raw populations.samples-raw.fa--> |
| 529 | 533 |
| 530 <!-- treemix populations.treemix --> | 534 <!-- treemix populations.treemix --> |
| 531 <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix"> | 535 <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix"> |
| 532 <filter>populations_output['treemix']</filter> | 536 <filter>populations_output['treemix']</filter> |
| 533 </data> | 537 </data> |
| 538 | |
| 539 <!-- gtf populations.treemix --> | |
| 540 <data format="gtf" name="out_gtf" label="${tool.name} on ${on_string} gtf" from_work_dir="stacks_outputs/populations.gtf"> | |
| 541 <filter>populations_output['gtf']</filter> | |
| 542 </data> | |
| 534 </xml> | 543 </xml> |
| 535 | 544 |
| 536 <!-- fastq output for kmer/clone-filter --> | 545 <!-- fastq output for kmer/clone-filter --> |
| 537 <xml name="fastq_output_filter"> | 546 <xml name="fastq_output_filter" token_format=""> |
| 538 <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}"> | 547 <data name="clean" format="@FORMAT@" label="${tool.name} on ${on_string}"> |
| 539 <filter>input_type['input_type_select'] == 'single'</filter> | 548 <filter>input_type['input_type_select'] == 'single'</filter> |
| 540 <yield/> | 549 <yield/> |
| 541 </data> | 550 </data> |
| 542 <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}"> | 551 <collection name="clean_pair" type="paired" format="@FORMAT@" label="${tool.name} on ${on_string}"> |
| 543 <filter>input_type['input_type_select'] == 'paired'</filter> | 552 <filter>input_type['input_type_select'] == 'paired'</filter> |
| 544 <yield/> | 553 <yield/> |
| 545 </collection> | 554 </collection> |
| 546 <data name="discarded" format_source="fqinputs" label="${tool.name} on ${on_string}: discarded reads"> | 555 <data name="discarded" format="@FORMAT@" label="${tool.name} on ${on_string}: discarded reads"> |
| 547 <filter>capture and input_type['input_type_select'] == 'single'</filter> | 556 <filter>capture and input_type['input_type_select'] == 'single'</filter> |
| 548 <yield/> | 557 <yield/> |
| 549 </data> | 558 </data> |
| 550 <collection name="discarded_pair" format_source="fqinputs" type="paired" label="${tool.name} on ${on_string}: discarded reads"> | 559 <collection name="discarded_pair" format="@FORMAT@" type="paired" label="${tool.name} on ${on_string}: discarded reads"> |
| 551 <filter>capture and input_type['input_type_select'] == 'paired'</filter> | 560 <filter>capture and input_type['input_type_select'] == 'paired'</filter> |
| 552 <yield/> | 561 <yield/> |
| 553 </collection> | 562 </collection> |
| 554 </xml> | 563 </xml> |
| 555 | 564 |