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comparison macros.xml @ 2:8a55d29c8fcf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Thu, 16 Jul 2020 07:28:45 -0400
parents 38c9f9a680f0
children 1544278c272e
comparison
equal deleted inserted replaced
1:38c9f9a680f0 2:8a55d29c8fcf
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement> 5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
6 <requirement type="package" version="3.7">python</requirement>
7 <requirement type="package" version="4.6.0">findutils</requirement>
6 <yield/> 8 <yield/>
7 </requirements> 9 </requirements>
8 </xml> 10 </xml>
9 11
10 <token name="@STACKS_VERSION@">2.4</token> 12 <token name="@STACKS_VERSION@">2.53</token>
11 <token name="@WRAPPER_VERSION@">1</token> 13 <token name="@WRAPPER_VERSION@">0</token>
12 <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 --> 14 <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
13 <token name="@PROFILE@">18.01</token> 15 <token name="@PROFILE@">18.01</token>
14 16
15 <xml name="citation"> 17 <xml name="citation">
16 <citations> 18 <citations>
105 </xml> 107 </xml>
106 108
107 <!-- log file handling --> 109 <!-- log file handling -->
108 <token name="@TEE_APPEND_LOG@"><![CDATA[ 110 <token name="@TEE_APPEND_LOG@"><![CDATA[
109 #if $output_log 111 #if $output_log
110 2>> '$output_log' && 112 2> '$output_log'
111 #end if
112 ]]></token>
113 <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
114 #if $output_log
115 cat '$output_log' 2>&1
116 #end if 113 #end if
117 ]]></token> 114 ]]></token>
118 <xml name="in_log"> 115 <xml name="in_log">
119 <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" /> 116 <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset"/>
120 </xml> 117 </xml>
121 <xml name="out_log"> 118 <xml name="out_log">
122 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> 119 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
123 <filter>add_log</filter> 120 <filter>add_log</filter>
124 </data> 121 </data>
125 </xml> 122 </xml>
126 123
127 <!-- inputs from previous pipeline steps --> 124 <!-- inputs from previous pipeline steps -->
128 <xml name="input_stacks_macro"> 125 <xml name="input_stacks_macro">
129 <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" /> 126 <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks"/>
130 </xml> 127 </xml>
131 <xml name="input_cat_macro"> 128 <xml name="input_cat_macro">
132 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> 129 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks"/>
133 </xml> 130 </xml>
134 <xml name="input_matches_macro"> 131 <xml name="input_matches_macro">
135 <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" /> 132 <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks"/>
136 </xml> 133 </xml>
137 <xml name="bam_input_macro"> 134 <xml name="bam_input_macro">
138 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" /> 135 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference"/>
139 </xml> 136 </xml>
140 <xml name="input_aln_macro"> 137 <xml name="input_aln_macro">
141 <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> 138 <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P"/>
142 </xml> 139 </xml>
143 140
144 <!-- code for creating links to the data sets from previous pipeline steps 141 <!-- code for creating links to the data sets from previous pipeline steps
145 - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv) 142 - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv)
146 also stores sample names in list (samples) 143 also stores sample names in list (samples)
193 <param name="input_type_select" type="select" label="Single-end or paired-end reads"> 190 <param name="input_type_select" type="select" label="Single-end or paired-end reads">
194 <option value="single" selected="True">Single-end files</option> 191 <option value="single" selected="True">Single-end files</option>
195 <option value="paired">Paired-end files</option> 192 <option value="paired">Paired-end files</option>
196 </param> 193 </param>
197 <when value="single"> 194 <when value="single">
198 <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="@MULTIPLE@" label="Singles-end reads" /> 195 <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="@MULTIPLE@" label="Singles-end reads"/>
199 <param name="barcode_encoding" type="select" label="Barcode location"> 196 <param name="barcode_encoding" type="select" label="Barcode location">
200 <expand macro="barcode_encoding_single" type="Barcode" /> 197 <expand macro="barcode_encoding_single" type="Barcode"/>
201 </param> 198 </param>
202 </when> 199 </when>
203 <when value="paired"> 200 <when value="paired">
204 <param name="fqinputs" type="data_collection" collection_type="@LISTTYPE@" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/> 201 <param name="fqinputs" type="data_collection" collection_type="@LISTTYPE@" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/>
205 <param name="barcode_encoding" type="select" label="Barcode location"> 202 <param name="barcode_encoding" type="select" label="Barcode location">
206 <expand macro="barcode_encoding_pair" type="Barcode" /> 203 <expand macro="barcode_encoding_pair" type="Barcode"/>
207 </param> 204 </param>
208 </when> 205 </when>
209 </conditional> 206 </conditional>
210 <yield/> 207 <yield/>
211 </xml> 208 </xml>
212 209
213 <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired"> 210 <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired">
214 <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@"> 211 <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
215 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" /> 212 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file"/>
216 </expand> 213 </expand>
217 </xml> 214 </xml>
218 215
219 <!-- fastq input (used in denovomap, tsv2bam, ustacks) 216 <!-- fastq input (used in denovomap, tsv2bam, ustacks)
220 - fastq_optional: makes fastq input optional (true/false) 217 - fastq_optional: makes fastq input optional (true/false)
390 387
391 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) --> 388 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) -->
392 <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools --> 389 <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools -->
393 <xml name="ustacks_outputs_macro" token_tooladd=""> 390 <xml name="ustacks_outputs_macro" token_tooladd="">
394 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci and polymorphism"> 391 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci and polymorphism">
395 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> 392 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs"/>
396 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> 393 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs"/>
397 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> 394 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs"/>
398 </collection> 395 </collection>
399 </xml> 396 </xml>
400 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv --> 397 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv -->
401 <xml name="cstacks_outputs_macro" token_tooladd=""> 398 <xml name="cstacks_outputs_macro" token_tooladd="">
402 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci"> 399 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci">
403 <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" /> 400 <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs"/>
404 </collection> 401 </collection>
405 </xml> 402 </xml>
406 <!-- sstacks outputs collection containing SAMPLE.matches.tsv --> 403 <!-- sstacks outputs collection containing SAMPLE.matches.tsv -->
407 <xml name="sstacks_outputs_macro" token_tooladd=""> 404 <xml name="sstacks_outputs_macro" token_tooladd="">
408 <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog"> 405 <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog">
409 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> 406 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs"/>
410 </collection> 407 </collection>
411 </xml> 408 </xml>
412 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam --> 409 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam -->
413 <xml name="tsv2bam_outputs_macro" token_tooladd=""> 410 <xml name="tsv2bam_outputs_macro" token_tooladd="">
414 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog (bam)"> 411 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog (bam)">
415 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" /> 412 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs"/>
416 </collection> 413 </collection>
417 </xml> 414 </xml>
418 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz 415 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz
419 + optional output alignments.bam (if no popmap is given) and POP.alns.bam otherwise--> 416 + optional output alignments.bam (if no popmap is given) and POP.alns.bam otherwise-->
420 <xml name="gstacks_outputs_full_macro" token_tooladd=""> 417 <xml name="gstacks_outputs_full_macro" token_tooladd="">
421 <expand macro="gstacks_outputs_macro"/> 418 <expand macro="gstacks_outputs_macro"/>
422 <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs"> 419 <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs">
423 <filter>add_log_distribs</filter> 420 <filter>add_log_distribs</filter>
424 </data> 421 </data>
425 <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments"> 422 <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
426 <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" ext="bam" directory="stacks_outputs" /> 423 <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" ext="bam" directory="stacks_outputs"/>
427 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter> 424 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter>
428 </collection> 425 </collection>
429 <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam"> 426 <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
430 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter> 427 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter>
431 </data> 428 </data>
432 </xml> 429 </xml>
433 <xml name="gstacks_outputs_macro" token_tooladd=""> 430 <xml name="gstacks_outputs_macro" token_tooladd="">
434 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites"> 431 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
435 <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" /> 432 <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/>
436 <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" /> 433 <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs"/>
437 </collection> 434 </collection>
438 </xml> 435 </xml>
439 436
440 <!-- default output of populations --> 437 <!-- default output of populations -->
441 <xml name="populations_output_light" token_tooladd=""> 438 <xml name="populations_output_light" token_tooladd="">
442 <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv" /> 439 <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv"/>
443 <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv" /> 440 <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv"/>
444 <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs" /> 441 <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs"/>
445 <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv" /> 442 <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv"/>
446 <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv" /> 443 <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv"/>
447 <data format="tabular" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" />
448 </xml> 444 </xml>
449 445
450 <xml name="populations_output_full"> 446 <xml name="populations_output_full">
451 <expand macro="populations_output_light"/> 447 <expand macro="populations_output_light"/>
448
449 <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
450 <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter>
451 </data>
452 452
453 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> 453 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
454 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> 454 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
455 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> 455 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
456 </data> 456 </data>
529 529
530 <!-- treemix populations.treemix --> 530 <!-- treemix populations.treemix -->
531 <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix"> 531 <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
532 <filter>populations_output['treemix']</filter> 532 <filter>populations_output['treemix']</filter>
533 </data> 533 </data>
534 </xml>
535
536 <!-- fastq output for kmer/clone-filter -->
537 <xml name="fastq_output_filter">
538 <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}">
539 <filter>input_type['input_type_select'] == 'single'</filter>
540 <yield/>
541 </data>
542 <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}">
543 <filter>input_type['input_type_select'] == 'paired'</filter>
544 <yield/>
545 </collection>
546 <data name="discarded" format_source="fqinputs" label="${tool.name} on ${on_string}: discarded reads">
547 <filter>capture and input_type['input_type_select'] == 'single'</filter>
548 <yield/>
549 </data>
550 <collection name="discarded_pair" format_source="fqinputs" type="paired" label="${tool.name} on ${on_string}: discarded reads">
551 <filter>capture and input_type['input_type_select'] == 'paired'</filter>
552 <yield/>
553 </collection>
534 </xml> 554 </xml>
535 555
536 <xml name="snp_options_alpha"> 556 <xml name="snp_options_alpha">
537 <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > 557 <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
538 <option value="0.1">0.1</option> 558 <option value="0.1">0.1</option>
552 <when value="snp"> 572 <when value="snp">
553 <expand macro="snp_options_alpha"/> 573 <expand macro="snp_options_alpha"/>
554 </when> 574 </when>
555 <when value="bounded"> 575 <when value="bounded">
556 <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound for epsilon, the error rate" help="between 0 and 1.0"/> 576 <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
557 <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0" /> 577 <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0"/>
558 <expand macro="snp_options_alpha"/> 578 <expand macro="snp_options_alpha"/>
559 </when> 579 </when>
560 <when value="fixed"> 580 <when value="fixed">
561 <yield/> 581 <yield/>
562 </when> 582 </when>
572 default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap) 592 default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
573 otherwise no default is is available and gstacks will output and error 593 otherwise no default is is available and gstacks will output and error
574 "Error: No value was provided for \-\-var-alpha and there is no default for this model)" 594 "Error: No value was provided for \-\-var-alpha and there is no default for this model)"
575 --> 595 -->
576 <xml name="variant_calling_options_vg" token_varalpha_default=""> 596 <xml name="variant_calling_options_vg" token_varalpha_default="">
577 <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." /> 597 <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available."/>
578 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" /> 598 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes"/>
579 </xml> 599 </xml>
580 600
581 <xml name="barcode_encoding_single" token_type=""> 601 <xml name="barcode_encoding_single" token_type="">
582 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option> 602 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option>
583 <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option> 603 <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option>