Mercurial > repos > iuc > stacks_refmap
diff macros.xml @ 0:66d3c1ae3937 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
| author | iuc |
|---|---|
| date | Tue, 14 Jun 2016 14:06:44 -0400 |
| parents | |
| children | 26ad8a52d9fd |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 14 14:06:44 2016 -0400 @@ -0,0 +1,376 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.40">stacks</requirement> + <requirement type="package" version="1.2.10">velvet</requirement> + <container type="docker">quay.io/mulled/stacks:1.40--1</container> + <yield/> + </requirements> + </xml> + + <token name="@WRAPPER_VERSION@">1.40</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://creskolab.uoregon.edu/stacks/>`_ + +`Stacks manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_ + +`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> + </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="@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_1.rqtl.tsv batch_1.genotypes.rqtl.tsv && + 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> + + <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_fastpĥase" 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 name="alpha" 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 name="bound_low" 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 name="bound_high" 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 name="alpha" 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 name="alpha" 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 name="bound_low" 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 name="bound_high" 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 name="alpha" 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 name="bc_err_freq" 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> +</macros>