Mercurial > repos > iuc > stacks2_populations

comparison stacks_populations.xml @ 1:9a44832748c5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:17:47 -0400
parents 6fba323a242d
children 38942a7e3801
comparison
equal deleted inserted replaced
0:6fba323a242d 1:9a44832748c5
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #import re 9 #import re
10 10
11 mkdir stacks_inputs stacks_outputs 11 mkdir stacks_inputs stacks_outputs &&
12 12
13 && 13 #if $output_log
14 ln -s '$output_log' stacks_outputs/populations.log &&
15 #end if
14 16
15 #if str($options_usage.input_type) == 'stacks' 17 #if str($options_usage.input_type) == 'stacks'
16 #for $input_file in $options_usage.input_aln 18 #for $input_file in $options_usage.input_aln
17 #set $filename = str($input_file.element_identifier) 19 #set $filename = str($input_file.element_identifier)
18 #if $filename == "catalog.calls" or $filename == "catalog.fa.gz": 20 #if $filename == "catalog.calls" or $filename == "catalog.fa.gz":
43 -batch_size '$batch_size' 45 -batch_size '$batch_size'
44 #end if 46 #end if
45 47
46 ## Data filtering 48 ## Data filtering
47 49
48 -p $options_filtering.minpop 50 --min-populations $options_filtering.minpop
49 -r $options_filtering.minperc 51 --min-samples-per-pop $options_filtering.minperc
50 -R $options_filtering.min_samples_overall 52 --min-samples-overall $options_filtering.min_samples_overall
51 $options_filtering.filter_haplotype_wise 53 $options_filtering.filter_haplotype_wise
52 --min_maf $options_filtering.min_maf 54 --min_maf $options_filtering.min_maf
53 --min_mac $options_filtering.min_mac 55 --min_mac $options_filtering.min_mac
54 #if str($options_filtering.max_obs_het) 56 #if str($options_filtering.max_obs_het)
55 --max_obs_het $options_filtering.max_obs_het 57 --max_obs_het $options_filtering.max_obs_het
141 #if str($options_usage.input_type) == 'vcf' 143 #if str($options_usage.input_type) == 'vcf'
142 #if $output_log 144 #if $output_log
143 > $output_log 145 > $output_log
144 #end if 146 #end if
145 && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done 147 && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done
146 #else
147 #if $output_log
148 && mv stacks_outputs/populations.log $output_log
149 #end if
150 #end if 148 #end if
151 ]]></command> 149 ]]></command>
152 150
153 <inputs> 151 <inputs>
154 <conditional name="options_usage"> 152 <conditional name="options_usage">
167 <param argument="--batch_size" type="integer" value="" optional="true" label="Number of loci to process in a batch" help="(default: 10,000 in de novo mode; in reference mode, one chromosome per batch). Increase to speed analysis, uses more memory, decrease to save memory)"/> 165 <param argument="--batch_size" type="integer" value="" optional="true" label="Number of loci to process in a batch" help="(default: 10,000 in de novo mode; in reference mode, one chromosome per batch). Increase to speed analysis, uses more memory, decrease to save memory)"/>
168 166
169 <!-- Data Filtering --> 167 <!-- Data Filtering -->
170 <section name="options_filtering" title="Data filtering options" expanded="true"> 168 <section name="options_filtering" title="Data filtering options" expanded="true">
171 169
172 <param name="minperc" argument="-r" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" /> 170 <param name="minperc" argument="--min-samples-per-pop" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" />
173 <param name="minpop" argument="-p" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus" /> 171 <param name="minpop" argument="--min-populations" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus" />
174 <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus" /> 172 <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus" />
175 <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data." /> 173 <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data." />
176 <param argument="--min_maf" type="float" value="0" min="0" max="0.5" label="Minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus" /> 174 <param argument="--min_maf" type="float" value="0" min="0" max="0.5" label="Minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus" />
177 <param argument="--min_mac" type="integer" value="0" min="0" label="Minimum minor allele count" help="specify a minimum minor allele count required to process a nucleotide site at a locus" /> 175 <param argument="--min_mac" type="integer" value="0" min="0" label="Minimum minor allele count" help="specify a minimum minor allele count required to process a nucleotide site at a locus" />
178 <param argument="--max_obs_het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus." /> 176 <param argument="--max_obs_het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus." />
429 <param name="min_mac" value="1"/> 427 <param name="min_mac" value="1"/>
430 <param name="max_obs_het" value="0.8" /> 428 <param name="max_obs_het" value="0.8" />
431 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> 429 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" />
432 </section> 430 </section>
433 <assert_command> 431 <assert_command>
434 <has_text text="-r 0.1" /> 432 <has_text text="--min-samples-per-pop 0.1" />
435 <has_text text="-p 2" /> 433 <has_text text="--min-populations 2" />
436 <has_text text="--min-samples-overall 0.01" /> 434 <has_text text="--min-samples-overall 0.01" />
437 <has_text text="--filter-haplotype-wise" /> 435 <has_text text="--filter-haplotype-wise" />
438 <has_text text="--min_maf 0.01" /> 436 <has_text text="--min_maf 0.01" />
439 <has_text text="--min_mac 1" /> 437 <has_text text="--min_mac 1" />
440 <has_text text="--max_obs_het 0.8" /> 438 <has_text text="--max_obs_het 0.8" />
464 <param name="minpop" value="2"/> 462 <param name="minpop" value="2"/>
465 <param name="min_samples_overall" value="0.01"/> 463 <param name="min_samples_overall" value="0.01"/>
466 <param name="min_maf" value="0.01" /> 464 <param name="min_maf" value="0.01" />
467 <param name="min_mac" value="1"/> 465 <param name="min_mac" value="1"/>
468 <param name="max_obs_het" value="0.8" /> 466 <param name="max_obs_het" value="0.8" />
469 <!-- since write_random_snp runs in ifinite loop switch to write_single --> 467 <!-- since write_random_snp runs in infinite loop switch to write_single -->
470 <param name="filter_single_snp" value="--write_single_snp"/> 468 <param name="filter_single_snp" value="--write_single_snp"/>
471 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> 469 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" />
472 </section> 470 </section>
473 <assert_command> 471 <assert_command>
474 <has_text text="-r 0.1" /> 472 <has_text text="--min-samples-per-pop 0.1" />
475 <has_text text="-p 2" /> 473 <has_text text="--min-populations 2" />
476 <has_text text="--min-samples-overall 0.01" /> 474 <has_text text="--min-samples-overall 0.01" />
477 <has_text text="--min_maf 0.01" /> 475 <has_text text="--min_maf 0.01" />
478 <has_text text="--min_mac 1" /> 476 <has_text text="--min_mac 1" />
479 <has_text text="--max_obs_het 0.8" /> 477 <has_text text="--max_obs_het 0.8" />
480 <has_text text="--write_random_snp" /> 478 <not_has_text text="--write_random_snp" />
481 <has_text text="-B " /> 479 <has_text text="-B " />
482 </assert_command> 480 </assert_command>
483 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> 481 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
484 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output> 482 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="" /></assert_contents></output>
485 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output> 483 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="" /></assert_contents></output>