Mercurial > repos > iuc > stacks2_tsv2bam

comparison macros.xml @ 3:a9c34a289493 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 09:28:24 +0000
parents bf0e43ab0416
children 69842dd5aa48
comparison
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2:bf0e43ab0416 3:a9c34a289493
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