Mercurial > repos > iuc > stacks_genotypes
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author | iuc |
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date | Fri, 07 Apr 2023 22:01:52 +0000 |
parents | 46f061f3cfeb |
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<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> <requirement type="package" version="1.46">stacks</requirement> <requirement type="package" version="1.2.10">velvet</requirement> <requirement type="package" version="1.1">stacks_summary</requirement> <yield/> </requirements> </xml> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">stacks</xref> </xrefs> </xml> <token name="@WRAPPER_VERSION@">1.46</token> <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> </stdio> </xml> <xml name="citation"> <citations> <citation type="doi">10.1111/mec.12354</citation> <citation type="doi">10.1111/mec.12330</citation> <citation type="doi">10.1534/g3.111.000240</citation> <citation type="doi">10.1534/genetics.111.127324</citation> <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> <citation type="doi">10.1073/pnas.1006538107</citation> </citations> </xml> <token name="@STACKS_INFOS@"> <![CDATA[ -------- **Created by:** Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko **Project links:** `Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_ `Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_ `Stacks google group <http://groups.google.com/group/stacks-users>`_ ]]></token> <xml name="enzymes"> <option value="aciI">aciI</option> <option value="ageI">ageI</option> <option value="aluI">aluI</option> <option value="apeKI">apeKI</option> <option value="apoI">apoI</option> <option value="aseI">aseI</option> <option value="bamHI">bamHI</option> <option value="bfaI">bfaI</option> <option value="bgIII">bgIII</option> <option value="bspDI">bspDI</option> <option value="bstYI">bstYI</option> <option value="claI">claI</option> <option value="ddeI">ddeI</option> <option value="dpnII">dpnII</option> <option value="eaeI">eaeI</option> <option value="ecoRI">ecoRI</option> <option value="ecoRV">ecoRV</option> <option value="ecoT22I">ecoT22I</option> <option value="hindIII">hindIII</option> <option value="kpnI">kpnI</option> <option value="mluCI">mluCI</option> <option value="mseI">mseI</option> <option value="mspI">mspI</option> <option value="ndeI">ndeI</option> <option value="nheI">nheI</option> <option value="nlaIII">nlaIII</option> <option value="notI">notI</option> <option value="nsiI">nsiI</option> <option value="pstI">pstI</option> <option value="rsaI">rsaI</option> <option value="sacI">sacI</option> <option value="sau3AI">sau3AI</option> <option value="sbfI">sbfI</option> <option value="sexAI">sexAI</option> <option value="sgrAI">sgrAI</option> <option value="speI">speI</option> <option value="sphI">sphI</option> <option value="taqI">taqI</option> <option value="xbaI">xbaI</option> <option value="xhoI">xhoI</option> <option value="csp6I">csp6I</option> <option value="bsaHI">bsaHI</option> <option value="hpaII">hpaII</option> <option value="ncoI">ncoI</option> <option value="ApaLI">ApaLI</option> </xml> <xml name="cross_types"> <option value="CP">CP (F1 cross)</option> <option value="F2">F2 (F2 cross)</option> <option value="BC1">BC1 (backcross)</option> <option value="DH">DH (double haploid cross)</option> <option value="GEN">GEN (generic, unspecific to any map type)</option> </xml> <token name="@CLEAN_EXT@"> <![CDATA[ #from os.path import splitext #import re #def clean_ext($identifier) #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam')) #set $identifier = splitext($identifier)[0] #end while $identifier#slurp #end def ]]> </token> <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@"> <![CDATA[ ## We need to do this as the output file names contains the value of an option (min progeny) && cd stacks_outputs/ && ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv && ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc && ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt && ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv && cd .. ]]> </token> <token name="@NORM_GENOTYPES_OUTPUT_FULL@"> <![CDATA[ ## We need to do this as the output file names contains the value of an option (min progeny) && cd stacks_outputs/ && ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv && ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt && ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv && ln -s batch_1.genotypes_*.rqtl.tsv batch_1.genotypes.rqtl.tsv && ln -s batch_1.haplotypes_*.tsv batch_1.haplotypes.tsv && ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc && ln -s batch_1.genotypes_*.txt batch_1.genotypes.txt && ln -s batch_1.genotypes_*[^rqtl].tsv batch_1.genotypes.tsv && cd .. ]]> </token> <xml name="genotypes_output_light"> <data format="txt" name="out_joinmap" label="Haplotypes table (JoinMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.loc"> <filter>options_usage['rad_analysis_type'] == "genetic"</filter> <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter> </data> <data format="tabular" name="out_generic_haplo" label="Haplotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"> <filter>options_usage['rad_analysis_type'] == "genetic"</filter> </data> <data format="tabular" name="out_generic_geno" label="Genotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.tsv"> <filter>options_usage['rad_analysis_type'] == "genetic"</filter> <filter>options_usage['cross_type'] == "GEN"</filter> </data> <data format="tabular" name="out_sql_markers" label="Markers table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"> <filter>options_usage['rad_analysis_type'] == "genetic"</filter> </data> <data format="tabular" name="out_sql_genotypes" label="Haplotypes table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.txt"> <filter>options_usage['rad_analysis_type'] == "genetic"</filter> </data> </xml> <xml name="genotypes_output_full"> <!-- Output formats generated by genotypes: JoinMap, default, only if map type is F2/BC1/DH/CP => batch_1.genotypes_1.loc OneMap, only if map type is F2/BC1 => batch_1.genotypes_1onemap.tsv OneMap/MapMaker, only if map type is CP => batch_1.genotypes_1.onemap.txt Genomic, for all map types => batch_1.genomic_1.tsv R/QTL, only if map type is F2/BC1/DH => batch_1.genotypes_1.rqtl.tsv Additional non-optional output (ie not altered by -o option): Generic format, for every map types => batch_1.haplotypes_1.tsv Generic format, if map type is GEN => batch_1.genotypes_1.tsv --> <data format="txt" name="out_joinmap" label="Haplotypes table (JoinMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.loc"> <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter> <filter>'map_out' not in options_usage or options_usage['map_out']['map_out_type'] == 'joinmap'</filter> </data> <data format="tabular" name="out_onemap" label="Haplotypes table (OneMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.onemap.txt"> <filter>options_usage['cross_type'] in ['F2', 'BC1']</filter> <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter> </data> <data format="tabular" name="out_onemap_mapmaker" label="Haplotypes table (OneMap/MapMaker format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.onemap.tsv"> <filter>options_usage['cross_type'] in ['CP']</filter> <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter> </data> <data format="tabular" name="out_genomic" label="Haplotypes table (Genomic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genomic.tsv"> <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'genomic'</filter> </data> <data format="tabular" name="out_rqtl" label="Haplotypes table (R/QTL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.rqtl.tsv"> <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH']</filter> <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'rqtl'</filter> </data> <data format="tabular" name="out_generic_haplo" label="Haplotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/> <data format="tabular" name="out_generic_geno" label="Genotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.tsv"> <filter>options_usage['cross_type'] == "GEN"</filter> </data> <data format="tabular" name="out_sql_markers" label="Markers table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"/> <data format="tabular" name="out_sql_genotypes" label="Haplotypes table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.txt"/> </xml> <xml name="populations_output_light"> <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"> <filter>options_usage['rad_analysis_type'] == "population"</filter> </data> <data format="tabular" name="out_hapstats" label="Haplotype-based summary statistics for each locus in each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hapstats.tsv"> <filter>options_usage['rad_analysis_type'] == "population"</filter> </data> <data format="tabular" name="out_populations_log" label="Populations log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.populations.log"> <filter>options_usage['rad_analysis_type'] == "population"</filter> </data> <data format="tabular" name="out_sumstats_sum" label="Summary of summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats_summary.tsv"> <filter>options_usage['rad_analysis_type'] == "population"</filter> </data> <data format="tabular" name="out_sumstats" label="Summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats.tsv"> <filter>options_usage['rad_analysis_type'] == "population"</filter> </data> <data format="tabular" name="out_sql" label="Stacks SQL format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"> <filter>options_usage['rad_analysis_type'] == "population"</filter> </data> </xml> <xml name="populations_output_full"> <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/> <data format="tabular" name="out_hapstats" label="Haplotype-based summary statistics for each locus in each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hapstats.tsv"/> <data format="tabular" name="out_populations_log" label="Populations log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.populations.log"/> <data format="tabular" name="out_sumstats_sum" label="Summary of summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats_summary.tsv"/> <data format="tabular" name="out_sumstats" label="Summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats.tsv"/> <data format="tabular" name="out_sql" label="Stacks SQL format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"/> <data format="tabular" name="out_fstats" label="SNP and Haplotype-based F statistics with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phistats.tsv"> <filter>fstats</filter> </data> <data format="tabular" name="out_fasta" label="Full sequence for each unique haplotype (regardless of plausibility) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fa"> <filter>populations_output['fasta']</filter> </data> <data format="tabular" name="out_phylip_all_partitions" label="Phylip all (partitions) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fullseq.partitions.phylip"> <filter>populations_output['phylip_var_all']</filter> </data> <data format="tabular" name="out_phylip_all_pop" label="Phylip all (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fullseq.phylip"> <filter>populations_output['phylip_var_all']</filter> </data> <data format="tabular" name="out_phylip_all_loci" label="Phylip all (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1fullseq.phylip.log"> <filter>populations_output['phylip_var_all']</filter> </data> <data format="tabular" name="out_genepop" label="GenePop formatwith ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genepop"> <filter>populations_output['genepop']</filter> </data> <data format="tabular" name="out_vcf_haplotypes" label="Haplotypes in VCF format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.vcf"> <filter>populations_output['vcf_haplotypes']</filter> </data> <data format="tabular" name="out_hzar" label="Genotypes in Hybrid Zone Analysis using R (HAZR) format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hzar.csv"> <filter>populations_output['hzar']</filter> </data> <data format="tabular" name="out_beagle_phased_haplotypes" label="Beagle format (phased, haplotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.phased.bgl"> <filter>populations_output['beagle_phased']</filter> </data> <data format="tabular" name="out_beagle_phased_markers" label="Beagle format (phased, markers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.phased.bgl.markers"> <filter>populations_output['beagle_phased']</filter> </data> <data format="tabular" name="out_beagle_haplotypes" label="Beagle format (haplotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.unphased.bgl"> <filter>populations_output['beagle']</filter> </data> <data format="tabular" name="out_beagle_markers" label="Beagle format (markers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.unphased.bgl.markers"> <filter>populations_output['beagle']</filter> </data> <data format="tabular" name="out_phylip_pop" label="Phylip (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip"> <filter>populations_output['phylip']</filter> </data> <data format="tabular" name="out_phylip_loci" label="Phylip (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip.log"> <filter>populations_output['phylip']</filter> </data> <data format="tabular" name="out_plink_markers" label="PLINK (makers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.plink.map"> <filter>populations_output['plink']</filter> </data> <data format="tabular" name="out_plink_genotypes" label="PLINK format (genotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.plink.ped"> <filter>populations_output['plink']</filter> </data> <data format="tabular" name="out_fasta_strict" label="Full sequence for each haplotype (only for biologically plausible loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.strict.fa"> <filter>populations_output['fasta_strict']</filter> </data> <data format="tabular" name="out_structure" label="Structure format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.structure.tsv"> <filter>populations_output['structure']</filter> </data> <data format="tabular" name="out_treemix_pop" label="TreeMix format (population) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.treemix"> <filter>populations_output['treemix']</filter> </data> <data format="tabular" name="out_treemix_loci" label="TreeMix format (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.treemix.log"> <filter>populations_output['treemix']</filter> </data> <data format="tabular" name="out_fastphase" label="fastPHASE format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.un.fastphase.inp"> <filter>populations_output['fastphase']</filter> </data> <data format="tabular" name="out_phase" label="PHASE format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.un.phase.inp"> <filter>populations_output['phase']</filter> </data> <data format="tabular" name="out_vcf" label="SNPs in VCF format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.vcf"> <filter>populations_output['vcf']</filter> </data> <data format="tabular" name="out_genomic" label="Each nucleotide position in all population members with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genomic.tsv"> <filter>populations_output['options_genomic']['genomic']</filter> </data> </xml> <xml name="snp_options"> <conditional name="select_model"> <param name="model_type" type="select" label="Choose the model"> <option value="snp" selected="true">SNP</option> <option value="bounded">Bounded SNP</option> <option value="fixed">Fixed</option> </param> <when value="snp"> <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> <option value="0.001">0.001</option> </param> </when> <when value="bounded"> <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"/> <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" /> <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> <option value="0.001">0.001</option> </param> </when> <when value="fixed"> </when> </conditional> </xml> <xml name="snp_options_full"> <conditional name="select_model"> <param name="model_type" type="select" label="Choose the model"> <option value="snp" selected="true">SNP</option> <option value="bounded">Bounded SNP</option> <option value="fixed">Fixed</option> </param> <when value="snp"> <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> <option value="0.001">0.001</option> </param> </when> <when value="bounded"> <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"/> <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" /> <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> <option value="0.001">0.001</option> </param> </when> <when value="fixed"> <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> </when> </conditional> </xml> <xml name="barcode_encoding_single"> <option value="--inline_null" selected="True">Barcode is inline with sequence</option> <option value="--index_null">Barcode is provided in FASTQ header</option> </xml> <xml name="barcode_encoding_pair"> <option value="--inline_null" selected="True">Barcode is inline with sequence</option> <option value="--null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> <option value="--index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> <option value="--inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> <option value="--index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> <option value="--inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> <option value="--index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option> </xml> </macros>