Mercurial > repos > iuc > stacks2_populations
comparison stacks_populations.xml @ 6:e2db212d64ad draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author | iuc |
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date | Thu, 14 Apr 2022 09:21:25 +0000 |
parents | 887cf585cafc |
children | 564c33e5c3e3 |
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5:7b881f5f5ad5 | 6:e2db212d64ad |
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1 <tool id="stacks2_populations" name="Stacks2: populations" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> | 1 <tool id="stacks2_populations" name="Stacks2: populations" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
2 <description>Calculate population-level summary statistics</description> | 2 <description>Calculate population-level summary statistics</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
117 $populations_output.fasta_samples | 117 $populations_output.fasta_samples |
118 $populations_output.vcf | 118 $populations_output.vcf |
119 $populations_output.genepop | 119 $populations_output.genepop |
120 $populations_output.structure | 120 $populations_output.structure |
121 $populations_output.radpainter | 121 $populations_output.radpainter |
122 ##$populations_output.phase | |
123 ##$populations_output.fastphase | |
124 $populations_output.plink | 122 $populations_output.plink |
125 $populations_output.hzar | 123 $populations_output.hzar |
126 $populations_output.phylip | 124 $populations_output.phylip |
127 $populations_output.phylip_var | 125 $populations_output.phylip_var |
128 ##$populations_output.phylip_var_all | 126 ##$populations_output.phylip_var_all |
233 <param argument="--fasta-samples" truevalue="--fasta-samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format"/> | 231 <param argument="--fasta-samples" truevalue="--fasta-samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format"/> |
234 <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/> | 232 <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/> |
235 <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/> | 233 <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/> |
236 <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/> | 234 <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/> |
237 <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/> | 235 <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/> |
238 <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format"/>--> | |
239 <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format"/> | |
240 <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/> | 236 <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/> |
241 <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/> | 237 <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/> |
242 <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/> | 238 <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/> |
243 <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/> | 239 <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/> |
244 <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip-var-all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation."/>--> | 240 <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip-var-all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation."/>--> |
358 <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"/> |
359 </collection> | 355 </collection> |
360 </param> | 356 </param> |
361 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> | 357 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> |
362 <param name="add_log" value="yes"/> | 358 <param name="add_log" value="yes"/> |
363 <param name="advanced_options|log_fst_comp" value="yes"/> | 359 <param name="advanced_options|log_fst_comp" value="true"/> |
364 <param name="fstats_conditional|fstats" value="yes"/> | 360 <param name="fstats_conditional|fstats" value="yes"/> |
365 <param name="populations_output|fasta_loci" value="yes"/> | 361 <param name="populations_output|fasta_loci" value="true"/> |
366 <param name="populations_output|fasta_samples" value="yes"/> | 362 <param name="populations_output|fasta_samples" value="true"/> |
367 <param name="populations_output|fasta_samples_raw" value="yes"/> | 363 <param name="populations_output|fasta_samples_raw" value="true"/> |
368 <param name="populations_output|phylip" value="yes"/> | 364 <param name="populations_output|phylip" value="true"/> |
369 <param name="populations_output|phylip_var" value="yes"/> | 365 <param name="populations_output|phylip_var" value="true"/> |
370 <param name="populations_output|genepop" value="yes"/> | 366 <param name="populations_output|genepop" value="true"/> |
371 <param name="populations_output|vcf" value="yes"/> | 367 <param name="populations_output|vcf" value="true"/> |
372 <param name="populations_output|hzar" value="yes"/> | 368 <param name="populations_output|hzar" value="true"/> |
373 <param name="populations_output|plink" value="yes"/> | 369 <param name="populations_output|plink" value="true"/> |
374 <param name="populations_output|structure" value="yes"/> | 370 <param name="populations_output|structure" value="true"/> |
375 <param name="populations_output|radpainter" value="yes"/> | 371 <param name="populations_output|radpainter" value="true"/> |
376 <param name="populations_output|treemix" value="yes"/> | 372 <param name="populations_output|treemix" value="true"/> |
377 <param name="populations_output|gtf" value="yes"/> | 373 <param name="populations_output|gtf" value="true"/> |
378 <assert_command> | 374 <assert_command> |
379 <has_text text="--log-fst-comp"/> | 375 <has_text text="--log-fst-comp"/> |
380 </assert_command> | 376 </assert_command> |
381 <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> |
382 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> | 378 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> |