--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jun 14 14:04:40 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>