Mercurial > repos > iuc > stacks_denovomap

annotate macros.xml @ 0:9d588fb2aee5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
author iuc
date Tue, 14 Jun 2016 14:07:29 -0400
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9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.40">stacks</requirement>
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6 <requirement type="package" version="1.2.10">velvet</requirement>
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7 <container type="docker">quay.io/mulled/stacks:1.40--1</container>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11
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12 <token name="@WRAPPER_VERSION@">1.40</token>
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13
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14 <xml name="stdio">
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15 <stdio>
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16 <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
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17 </stdio>
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18 </xml>
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19
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20 <xml name="citation">
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21 <citations>
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22 <citation type="doi">10.1111/mec.12354</citation>
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23 <citation type="doi">10.1111/mec.12330</citation>
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24 <citation type="doi">10.1534/g3.111.000240</citation>
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25 <citation type="doi">10.1534/genetics.111.127324</citation>
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26 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
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27 <citation type="doi">10.1073/pnas.1006538107</citation>
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28 </citations>
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29 </xml>
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30
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31 <token name="@STACKS_INFOS@">
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32 <![CDATA[
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33 --------
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34
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35 **Created by:**
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36
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37 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko
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38
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39 **Project links:**
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40
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41 `Stacks website <http://creskolab.uoregon.edu/stacks/>`_
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42
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43 `Stacks manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_
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44
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45 `Stacks google group <http://groups.google.com/group/stacks-users>`_
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46 ]]></token>
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47
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48 <xml name="enzymes">
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49 <option value="aciI">aciI</option>
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50 <option value="ageI">ageI</option>
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51 <option value="aluI">aluI</option>
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52 <option value="apeKI">apeKI</option>
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53 <option value="apoI">apoI</option>
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54 <option value="aseI">aseI</option>
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55 <option value="bamHI">bamHI</option>
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56 <option value="bfaI">bfaI</option>
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57 <option value="bgIII">bgIII</option>
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58 <option value="bspDI">bspDI</option>
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59 <option value="bstYI">bstYI</option>
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60 <option value="claI">claI</option>
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61 <option value="ddeI">ddeI</option>
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62 <option value="dpnII">dpnII</option>
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63 <option value="eaeI">eaeI</option>
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64 <option value="ecoRI">ecoRI</option>
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65 <option value="ecoRV">ecoRV</option>
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66 <option value="ecoT22I">ecoT22I</option>
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67 <option value="hindIII">hindIII</option>
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68 <option value="kpnI">kpnI</option>
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69 <option value="mluCI">mluCI</option>
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70 <option value="mseI">mseI</option>
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71 <option value="mspI">mspI</option>
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72 <option value="ndeI">ndeI</option>
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73 <option value="nheI">nheI</option>
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74 <option value="nlaIII">nlaIII</option>
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75 <option value="notI">notI</option>
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76 <option value="nsiI">nsiI</option>
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77 <option value="pstI">pstI</option>
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78 <option value="rsaI">rsaI</option>
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79 <option value="sacI">sacI</option>
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80 <option value="sau3AI">sau3AI</option>
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81 <option value="sbfI">sbfI</option>
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82 <option value="sexAI">sexAI</option>
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83 <option value="sgrAI">sgrAI</option>
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84 <option value="speI">speI</option>
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85 <option value="sphI">sphI</option>
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86 <option value="taqI">taqI</option>
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87 <option value="xbaI">xbaI</option>
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88 <option value="xhoI">xhoI</option>
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89 </xml>
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90
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91 <xml name="cross_types">
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92 <option value="CP">CP (F1 cross)</option>
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93 <option value="F2">F2 (F2 cross)</option>
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94 <option value="BC1">BC1 (backcross)</option>
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95 <option value="DH">DH (double haploid cross)</option>
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96 <option value="GEN">GEN (generic, unspecific to any map type)</option>
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97 </xml>
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98
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99 <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@">
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100 <![CDATA[
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101 ## We need to do this as the output file names contains the value of an option (min progeny)
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102 &&
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103 cd stacks_outputs/ &&
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104 ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv &&
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105 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
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106 ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt &&
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107 ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv &&
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108 cd ..
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109 ]]>
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110 </token>
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111
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112 <token name="@NORM_GENOTYPES_OUTPUT_FULL@">
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113 <![CDATA[
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114 ## We need to do this as the output file names contains the value of an option (min progeny)
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115 &&
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116 cd stacks_outputs/ &&
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117 ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv &&
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118 ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt &&
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119 ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv &&
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120 ln -s batch_1.genotypes_1.rqtl.tsv batch_1.genotypes.rqtl.tsv &&
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121 ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv &&
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122 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
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123 ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt &&
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124 ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv &&
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125 cd ..
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126 ]]>
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127 </token>
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128
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129 <xml name="genotypes_output_light">
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130
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131 <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">
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132 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
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133 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter>
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134 </data>
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135
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136 <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">
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137 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
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138 </data>
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139 <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">
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140 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
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141 <filter>options_usage['cross_type'] == "GEN"</filter>
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142 </data>
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143
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144 <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">
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145 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
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146 </data>
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147
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148 <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">
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149 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
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150 </data>
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151 </xml>
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152
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153 <xml name="genotypes_output_full">
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154 <!-- Output formats generated by genotypes:
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155
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156 JoinMap, default, only if map type is F2/BC1/DH/CP => batch_1.genotypes_1.loc
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157 OneMap, only if map type is F2/BC1 => batch_1.genotypes_1onemap.tsv
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158 OneMap/MapMaker, only if map type is CP => batch_1.genotypes_1.onemap.txt
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159 Genomic, for all map types => batch_1.genomic_1.tsv
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160 R/QTL, only if map type is F2/BC1/DH => batch_1.genotypes_1.rqtl.tsv
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161
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162 Additional non-optional output (ie not altered by -o option):
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163
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164 Generic format, for every map types => batch_1.haplotypes_1.tsv
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165 Generic format, if map type is GEN => batch_1.genotypes_1.tsv -->
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166
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167 <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">
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168 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter>
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169 <filter>'map_out' not in options_usage or options_usage['map_out']['map_out_type'] == 'joinmap'</filter>
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170 </data>
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171
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172 <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">
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173 <filter>options_usage['cross_type'] in ['F2', 'BC1']</filter>
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174 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter>
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175 </data>
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176
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177 <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">
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178 <filter>options_usage['cross_type'] in ['CP']</filter>
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179 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter>
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180 </data>
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181
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182 <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">
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183 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'genomic'</filter>
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184 </data>
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185
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186 <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">
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187 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH']</filter>
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188 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'rqtl'</filter>
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189 </data>
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190
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191 <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"/>
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192
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193 <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">
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194 <filter>options_usage['cross_type'] == "GEN"</filter>
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195 </data>
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196
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197 <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"/>
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198
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199 <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"/>
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200 </xml>
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201
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202 <xml name="populations_output_light">
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203 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv">
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204 <filter>options_usage['rad_analysis_type'] == "population"</filter>
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205 </data>
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206
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207 <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">
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208 <filter>options_usage['rad_analysis_type'] == "population"</filter>
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209 </data>
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210
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211 <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">
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212 <filter>options_usage['rad_analysis_type'] == "population"</filter>
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213 </data>
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214
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215 <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">
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216 <filter>options_usage['rad_analysis_type'] == "population"</filter>
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217 </data>
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218
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219 <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">
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220 <filter>options_usage['rad_analysis_type'] == "population"</filter>
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221 </data>
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222
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223 <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">
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224 <filter>options_usage['rad_analysis_type'] == "population"</filter>
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225 </data>
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226 </xml>
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227
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228 <xml name="populations_output_full">
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229 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/>
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230
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231 <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"/>
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232
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233 <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"/>
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234
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235 <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"/>
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236
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237 <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"/>
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238
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239 <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"/>
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240
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241 <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">
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242 <filter>fstats</filter>
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243 </data>
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244 <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">
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245 <filter>populations_output['fasta']</filter>
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246 </data>
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247 <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">
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248 <filter>populations_output['phylip_var_all']</filter>
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249 </data>
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250 <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">
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251 <filter>populations_output['phylip_var_all']</filter>
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252 </data>
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253 <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">
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254 <filter>populations_output['phylip_var_all']</filter>
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255 </data>
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256 <data format="tabular" name="out_genepop" label="GenePop formatwith ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genepop">
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257 <filter>populations_output['genepop']</filter>
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258 </data>
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259 <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">
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260 <filter>populations_output['vcf_haplotypes']</filter>
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261 </data>
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262 <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">
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263 <filter>populations_output['hzar']</filter>
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264 </data>
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265 <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">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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266 <filter>populations_output['beagle_phased']</filter>
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267 </data>
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268 <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">
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269 <filter>populations_output['beagle_phased']</filter>
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270 </data>
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271 <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">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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272 <filter>populations_output['beagle']</filter>
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273 </data>
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274 <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">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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275 <filter>populations_output['beagle']</filter>
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276 </data>
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277 <data format="tabular" name="out_phylip_pop" label="Phylip (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip">
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278 <filter>populations_output['phylip']</filter>
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279 </data>
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280 <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">
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281 <filter>populations_output['phylip']</filter>
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282 </data>
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283 <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">
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284 <filter>populations_output['plink']</filter>
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285 </data>
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286 <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">
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287 <filter>populations_output['plink']</filter>
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288 </data>
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289 <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">
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290 <filter>populations_output['fasta_strict']</filter>
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291 </data>
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292 <data format="tabular" name="out_structure" label="Structure format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.structure.tsv">
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293 <filter>populations_output['structure']</filter>
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294 </data>
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295 <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">
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296 <filter>populations_output['treemix']</filter>
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297 </data>
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298 <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">
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299 <filter>populations_output['treemix']</filter>
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300 </data>
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301 <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">
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302 <filter>populations_output['fastphase']</filter>
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303 </data>
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304 <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">
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305 <filter>populations_output['phase']</filter>
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306 </data>
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307 <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">
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308 <filter>populations_output['vcf']</filter>
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309 </data>
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310 <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">
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311 <filter>populations_output['options_genomic']['genomic']</filter>
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312 </data>
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313
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314 </xml>
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315
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316 <xml name="snp_options">
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317 <conditional name="select_model">
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318 <param name="model_type" type="select" label="Choose the model">
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319 <option value="snp" selected="true">SNP</option>
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320 <option value="bounded">Bounded SNP</option>
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321 <option value="fixed">Fixed</option>
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322 </param>
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323 <when value="snp">
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324 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
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325 <option value="0.1">0.1</option>
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326 <option value="0.05" selected="True">0.05</option>
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327 <option value="0.01">0.01</option>
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328 <option value="0.001">0.001</option>
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329 </param>
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330 </when>
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331 <when value="bounded">
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332 <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"/>
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333 <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" />
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334 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
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335 <option value="0.1">0.1</option>
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336 <option value="0.05" selected="True">0.05</option>
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337 <option value="0.01">0.01</option>
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338 <option value="0.001">0.001</option>
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339 </param>
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340 </when>
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341 <when value="fixed">
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342 </when>
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343 </conditional>
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344 </xml>
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345
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346 <xml name="snp_options_full">
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347 <conditional name="select_model">
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348 <param name="model_type" type="select" label="Choose the model">
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349 <option value="snp" selected="true">SNP</option>
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350 <option value="bounded">Bounded SNP</option>
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351 <option value="fixed">Fixed</option>
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352 </param>
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353 <when value="snp">
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354 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
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355 <option value="0.1">0.1</option>
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356 <option value="0.05" selected="True">0.05</option>
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357 <option value="0.01">0.01</option>
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358 <option value="0.001">0.001</option>
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359 </param>
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360 </when>
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361 <when value="bounded">
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362 <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"/>
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363 <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" />
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364 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
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365 <option value="0.1">0.1</option>
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366 <option value="0.05" selected="True">0.05</option>
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367 <option value="0.01">0.01</option>
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368 <option value="0.001">0.001</option>
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369 </param>
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370 </when>
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371 <when value="fixed">
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372 <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"/>
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373 </when>
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374 </conditional>
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375 </xml>
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376 </macros>