Mercurial > repos > iuc > stacks_rxstacks

annotate stacks_rxstacks.xml @ 4:fec69a2d92d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
author iuc
date Mon, 26 Sep 2016 11:45:25 -0400
parents 55814b6afe69
children 1919e1ecb90d
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1 <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0">
0
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2 <description>make corrections to genotype and haplotype calls</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command><![CDATA[
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10 mkdir stacks_inputs stacks_outputs
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12 &&
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14 #for $input_file in $input_col:
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15 #set $ext = ""
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16 #if not str($input_file.element_identifier).endswith('.tsv'):
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17 #set $ext = ".tsv"
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18 #end if
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19 ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" &&
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20 #end for
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22 rxstacks
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24 -t \${GALAXY_SLOTS:-1}
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26 -P stacks_inputs
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27
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28 ## Batch description
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29 -b 1
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30
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31 #if str($options_filtering.lnl):
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32 --lnl_filter
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33 --lnl_lim $options_filtering.lnl
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34 #end if
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35
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36 $options_filtering.lnl_dist
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37
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38 #if str($options_filtering.conf):
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39 --conf_filter
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40 --conf_lim $options_filtering.conf
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41 #end if
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42
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43 #if $options_filtering.prune.prune_haplo:
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44 --prune_haplo
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45 #if str($options_filtering.prune.max_haplo):
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46 --max_haplo $options_filtering.prune.max_haplo
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47 #end if
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48 #end if
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49
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50 ## snp_model
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51 #if str( $snp_options.select_model.model_type) == "bounded":
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52 --model_type bounded
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53 --bound_low $snp_options.select_model.bound_low
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54 --bound_high $snp_options.select_model.bound_high
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55 --alpha $snp_options.select_model.alpha
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56 #else if str( $snp_options.select_model.model_type) == "snp":
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57 --model_type snp
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58 --alpha $snp_options.select_model.alpha
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59 #else
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60 --model_type fixed
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61 #end if
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62
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63 -o stacks_outputs
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64 ]]></command>
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65
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66 <inputs>
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67 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" />
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68
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69 <section name="options_filtering" title="Data filtering options" expanded="true">
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70 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />
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71 <param name="lnl_dist" argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." />
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72
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73 <param name="conf" type="float" value="0.75" optional="true" argument="--conf_lim" min="0.0" max="1.0" label="Proportion of loci in population that must be confounded relative to the catalog locus (between 0.0 and 1.0)."/>
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74
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75 <conditional name="prune">
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76 <param name="prune_haplo" argument="--prune_haplo" type="boolean" checked="false" label="Prune out non-biological haplotypes unlikely to occur in the population." />
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77 <when value="false"></when>
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78 <when value="true">
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79 <param name="max_haplo" argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/>
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80 </when>
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81 </conditional>
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82 </section>
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83
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84 <!-- SNP Model options -->
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85 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
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86 <expand macro="snp_options"/>
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87 </section>
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88 </inputs>
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89
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90 <outputs>
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91 <data format="txt" name="output_log" label="rxstacks.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.rxstacks.log" />
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92
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93 <data format="txt" name="output_lnl_dist" label="Distribution of mean log likelihoods with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.rxstacks_lnls.tsv">
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94 <filter>options_filtering['lnl_dist']</filter>
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95 </data>
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96
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97 <collection name="tags" type="list" label="Assembled loci filtered from ${on_string}">
3
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98 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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99 </collection>
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100
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101 <collection name="snps" type="list" label="Model calls from each locus filtered from ${on_string}">
3
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102 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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103 </collection>
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104
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105 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus filtered from ${on_string}">
3
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106 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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107 </collection>
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108
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109 <collection name="all_output" type="list" label="Full output from rxstacks on ${on_string}">
3
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110 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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111 </collection>
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112 </outputs>
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113
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114 <tests>
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115 <test>
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116 <param name="input_col">
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117 <collection type="list">
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118 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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119 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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120 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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121 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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122 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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123 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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124 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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125 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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126 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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127 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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128 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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129 </collection>
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130 </param>
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131 <param name="options_filtering|lnl" value="-10.0" />
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132 <param name="options_filtering|lnl_dist" value="true" />
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133 <param name="options_filtering|prune_haplo" value="true" />
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134 <param name="options_filtering|max_haplo" value="1" />
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135
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136 <output name="output_log">
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137 <assert_contents>
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138 <has_text text="rxstacks executed" />
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139 </assert_contents>
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140 </output>
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141
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142 <output name="output_lnl_dist">
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143 <assert_contents>
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144 <has_text text="Median" />
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145 </assert_contents>
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146 </output>
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147
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148 <!-- samples -->
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149 <output_collection name="tags">
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150 <element name="PopA_01.tags">
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151 <assert_contents>
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152 <has_text text="lane1_fakedata7_0" />
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153 </assert_contents>
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154 </element>
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155 </output_collection>
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156 <output_collection name="snps">
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157 <element name="PopA_01.snps">
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158 <assert_contents>
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159 <has_text text="24.950" />
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160 </assert_contents>
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161 </element>
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162 </output_collection>
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163 <output_collection name="alleles">
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164 <element name="PopA_01.alleles">
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165 <assert_contents>
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166 <has_text text="AC" />
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167 </assert_contents>
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168 </element>
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169 </output_collection>
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170 </test>
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171 </tests>
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172
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173 <help>
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174 <![CDATA[
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175 .. class:: infomark
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176
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177 **What it does**
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178
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179 This program will run each of the Stacks components: first, running ustacks on each of the samples specified, building loci and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci that were marked as 'parents' or 'samples' on the command line, and finally, sstacks will be executed to match each sample against the catalog. A bit more detail on this process can be found in the FAQ. The denovo_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching, the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
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180
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181 --------
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182
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183 **Input files**
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184
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185 Output from denovo_map or ref_map
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186
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187 **Output files**
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188
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189 - XXX.tags.tsv file:
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190
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191 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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192
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193 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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194
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195
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196 - XXX.snps.tsv file:
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197
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198 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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199
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200 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
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201
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202
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203 - XXX.alleles.tsv file:
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204
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205 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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206
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207 - XXX.matches.tsv file:
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208
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209 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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210
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211 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
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212
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213 @STACKS_INFOS@
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214 ]]>
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215 </help>
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216 <expand macro="citation" />
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217 </tool>