Mercurial > repos > iuc > stacks_denovomap

annotate stacks_denovomap.xml @ 3:bab631cc9f64 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:28:47 -0400
parents 9d588fb2aee5
children 998dfec32bde
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3
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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1 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.1">
0
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2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</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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9 #from os.path import splitext
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10 #import re
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11
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12 #if str( $options_usage.rad_analysis_type ) == "genetic":
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13 #for $input_parent in $options_usage.parent_sequences:
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15 #if $input_parent.ext == "fastqsanger":
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16 #set $data_path = splitext($input_parent.element_identifier)[0]
0
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17 #set $data_path = re.sub(r'\.1$', '', $data_path)
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18 #set $data_path = $data_path + ".fq"
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19 #else:
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20 #set $data_path = splitext($input_parent.element_identifier)[0]
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21 #set $data_path = re.sub(r'\.1$', '', $data_path)
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22 #set $data_path = $data_path + ".fa"
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23 #end if
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25 ln -s "${input_parent}" "${data_path}" &&
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26 #end for
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28 #for $input_progeny in $options_usage.progeny_sequences:
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29 #if $input_progeny:
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30 #if $input_progeny.ext == "fastqsanger":
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31 #set $data_path = splitext($input_progeny.element_identifier)[0]
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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32 #set $data_path = re.sub(r'\.1$', '', $data_path)
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33 #set $data_path = $data_path + ".fq"
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34 #else:
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35 #set $data_path = splitext($input_progeny.element_identifier)[0]
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36 #set $data_path = re.sub(r'\.1$', '', $data_path)
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37 #set $data_path = $data_path + ".fa"
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38 #end if
0
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39
3
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40 ln -s "${input_progeny}" "${data_path}" &&
0
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41 #end if
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42 #end for
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43 #else:
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44 #for $input_indiv in $options_usage.individual_sample:
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45
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46 #if $input_indiv.ext == "fastqsanger":
3
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47 #set $data_path = splitext($input_indiv.element_identifier)[0]
0
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48 #set $data_path = re.sub(r'\.1$', '', $data_path)
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49 #set $data_path = $data_path + ".fq"
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50 #else:
3
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51 #set $data_path = splitext($input_indiv.element_identifier)[0]
0
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52 #set $data_path = re.sub(r'\.1$', '', $data_path)
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53 #set $data_path = $data_path + ".fa"
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54 #end if
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56 ln -s "${input_indiv}" "${data_path}" &&
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57 #end for
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58 #end if
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60 mkdir stacks_outputs
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61
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62 &&
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64 denovo_map.pl
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66 -T \${GALAXY_SLOTS:-1}
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67
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68 #if str( $options_usage.rad_analysis_type ) == "genetic":
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69 #for $input_parent in $options_usage.parent_sequences:
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70 #if $input_parent.ext == "fastqsanger":
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71 #set $data_path = splitext($input_parent.element_identifier)[0]
0
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72 #set $data_path = re.sub(r'\.1$', '', $data_path)
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73 #set $data_path = $data_path + ".fq"
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74 #else:
3
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75 #set $data_path = splitext($input_parent.element_identifier)[0]
0
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76 #set $data_path = re.sub(r'\.1$', '', $data_path)
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77 #set $data_path = $data_path + ".fa"
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78 #end if
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79
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80 -p "${data_path}"
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81 #end for
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82
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83 -A $options_usage.cross_type
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84
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85 #for $input_progeny in $options_usage.progeny_sequences:
3
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86 #if $input_progeny:
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87 #if $input_progeny.ext == "fastqsanger":
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88 #set $data_path = splitext($input_progeny.element_identifier)[0]
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89 #set $data_path = re.sub(r'\.1$', '', $data_path)
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90 #set $data_path = $data_path + ".fq"
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91 #else:
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92 #set $data_path = splitext($input_progeny.element_identifier)[0]
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93 #set $data_path = re.sub(r'\.1$', '', $data_path)
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94 #set $data_path = $data_path + ".fa"
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95 #end if
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96
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97 -r "${data_path}"
0
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98 #end if
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99 #end for
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100
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101 #if str($assembly_options.P):
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102 -P $assembly_options.P
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103 #end if
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104 #else:
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105 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample):
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106
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107 #if $input_indiv.ext == "fastqsanger":
3
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108 #set $data_path = splitext($input_indiv.element_identifier)[0]
0
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109 #set $data_path = re.sub(r'\.1$', '', $data_path)
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110 #set $data_path = $data_path + ".fq"
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111 #else:
3
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112 #set $data_path = splitext($input_indiv.element_identifier)[0]
0
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113 #set $data_path = re.sub(r'\.1$', '', $data_path)
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114 #set $data_path = $data_path + ".fa"
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115 #end if
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116
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117 -s "${data_path}"
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118 #end for
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119 -O "$options_usage.popmap"
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120 #end if
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121
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122 #if str($assembly_options.m):
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123 -m $assembly_options.m
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124 #end if
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125 #if str($assembly_options.N):
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126 -N $assembly_options.N
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127 #end if
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128 -M $assembly_options.M
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129 -n $assembly_options.n
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130 -t $assembly_options.t
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131 -H $assembly_options.H
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132
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133 ## Batch description
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134 -b 1
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135
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136 ## No SQL recording
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137 -S
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138
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139 ## snp_model
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140 #if str( $snp_options.select_model.model_type) == "bounded":
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141 --bound_low $snp_options.select_model.bound_low
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142 --bound_high $snp_options.select_model.bound_high
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143 --alpha $snp_options.select_model.alpha
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144 #else if str( $snp_options.select_model.model_type) == "snp":
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145 --alpha $snp_options.select_model.alpha
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146 #end if
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147
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148 -o stacks_outputs
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149
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150 #if str( $options_usage.rad_analysis_type ) == "genetic":
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151 @NORM_GENOTYPES_OUTPUT_LIGHT@
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152 #end if
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153 ]]></command>
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154
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155 <inputs>
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156 <conditional name="options_usage">
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157 <param name="rad_analysis_type" type="select" label="Select your usage">
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158 <option value="genetic" selected="true">Genetic map</option>
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159 <option value="population">Population</option>
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160 </param>
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161 <when value="genetic">
3
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162 <param name="parent_sequences" argument="-p" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing parent sequences" help="Files containing parent sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
0
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163
3
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164 <param name="progeny_sequences" argument="-r" format="fastqsanger,fasta" type="data" multiple="true" optional="true" label="Files containing progeny sequences" help="files containing progeny sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
0
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165
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166 <param name="cross_type" argument="-A" type="select" label="Cross type">
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167 <expand macro="cross_types"/>
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168 </param>
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169 </when>
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170 <when value="population">
3
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171 <param name="individual_sample" argument="-s" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing an individual sample from a population" help="files containing an individual sample from a population (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
0
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172 <param name="popmap" argument="-O" type="data" format="tabular,txt" label="Specify a population map" />
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173 </when>
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174 </conditional>
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175
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176 <!-- stack assembly options -->
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177 <section name="assembly_options" title="Assembly options" expanded="false">
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178 <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" />
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179 <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
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180 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
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181 <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
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182 <param name="n" argument="-n" type="integer" value="1" label="specify the number of mismatches allowed between loci when building the catalog"/>
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183
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184 <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
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185 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
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186 </section>
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187
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188 <!-- SNP Model options -->
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189 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
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190 <expand macro="snp_options"/>
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191 </section>
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192 </inputs>
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193 <outputs>
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194 <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" />
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195
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196 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
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197 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
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198 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
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199
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200 <expand macro="genotypes_output_light"/>
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201 <expand macro="populations_output_light"/>
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202
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203 <collection name="tags" type="list" label="Assembled loci from ${on_string}">
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204 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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205 </collection>
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206
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207 <collection name="snps" type="list" label="Model calls from each locus on ${on_string}">
3
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208 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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209 </collection>
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210
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211 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}">
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212 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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213 </collection>
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214
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215 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
3
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216 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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217 </collection>
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218
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219 <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}">
3
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220 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" />
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221 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />
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222 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)$" ext="txt" directory="stacks_outputs" />
0
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223 </collection>
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224 </outputs>
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225
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226 <tests>
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227 <test>
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228 <param name="options_usage|rad_analysis_type" value="genetic"/>
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229 <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
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230 <output name="output_log">
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231 <assert_contents>
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232 <has_text text="denovo_map.pl completed" />
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233 </assert_contents>
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234 </output>
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235
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236 <!-- catalog -->
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237 <output name="catalogtags">
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238 <assert_contents>
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239 <has_text text="catalog generated on" />
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240 </assert_contents>
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241 </output>
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242 <output name="catalogsnps">
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243 <assert_contents>
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244 <has_text text="catalog generated on" />
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245 </assert_contents>
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246 </output>
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247 <output name="catalogalleles">
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248 <assert_contents>
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249 <has_text text="catalog generated on" />
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250 </assert_contents>
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251 </output>
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252
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253 <!-- genotypes -->
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254 <output name="out_generic_haplo">
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255 <assert_contents>
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256 <has_text text="Catalog ID" />
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257 </assert_contents>
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258 </output>
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259 <output name="out_sql_markers">
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260 <assert_contents>
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261 <has_text text="Total Genotypes" />
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iuc
parents: 0
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262 </assert_contents>
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iuc
parents: 0
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263 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
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264 <output name="out_joinmap">
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iuc
parents: 0
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265 <assert_contents>
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iuc
parents: 0
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266 <has_text text="batch_1.genotypes_" />
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iuc
parents: 0
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267 </assert_contents>
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iuc
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268 </output>
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iuc
parents: 0
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269 <output name="out_sql_genotypes">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
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270 <assert_contents>
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iuc
parents: 0
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271 <has_text text="SQL ID" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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272 </assert_contents>
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iuc
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273 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
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274
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
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275 <!-- samples -->
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iuc
parents: 0
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276 <output_collection name="tags">
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iuc
parents: 0
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277 <element name="PopA_01.tags">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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278 <assert_contents>
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iuc
parents: 0
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279 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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280 </assert_contents>
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iuc
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281 </element>
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iuc
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282 </output_collection>
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iuc
parents: 0
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283 <output_collection name="snps">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
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284 <element name="PopA_01.snps">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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285 <assert_contents>
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iuc
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286 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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287 </assert_contents>
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288 </element>
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iuc
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289 </output_collection>
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iuc
parents: 0
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290 <output_collection name="alleles">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
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291 <element name="PopA_01.alleles">
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292 <assert_contents>
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iuc
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293 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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294 </assert_contents>
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295 </element>
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iuc
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296 </output_collection>
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iuc
parents: 0
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297 <output_collection name="matches">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
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298 <element name="PopA_01.matches">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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299 <assert_contents>
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iuc
parents: 0
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300 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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301 </assert_contents>
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iuc
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302 </element>
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iuc
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303 </output_collection>
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iuc
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304 </test>
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iuc
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305
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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306 <test>
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307 <param name="options_usage|rad_analysis_type" value="genetic"/>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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308 <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
0
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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309 <param name="options_usage|progeny_sequences" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
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iuc
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310 <output name="output_log">
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iuc
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311 <assert_contents>
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iuc
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312 <has_text text="denovo_map.pl completed" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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313 </assert_contents>
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314 </output>
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iuc
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315
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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316 <!-- catalog -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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317 <output name="catalogtags">
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iuc
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318 <assert_contents>
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iuc
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319 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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320 </assert_contents>
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321 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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322 <output name="catalogsnps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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323 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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324 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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325 </assert_contents>
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326 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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327 <output name="catalogalleles">
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iuc
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328 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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329 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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330 </assert_contents>
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331 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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332
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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333 <!-- genotypes -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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334 <output name="out_generic_haplo">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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335 <assert_contents>
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iuc
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336 <has_text text="Catalog ID" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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337 </assert_contents>
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338 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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339 <output name="out_sql_markers">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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340 <assert_contents>
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iuc
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341 <has_text text="Total Genotypes" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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342 </assert_contents>
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343 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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344 <output name="out_joinmap">
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iuc
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345 <assert_contents>
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iuc
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346 <has_text text="batch_1.genotypes_" />
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347 </assert_contents>
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348 </output>
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iuc
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349 <output name="out_sql_genotypes">
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iuc
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350 <assert_contents>
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iuc
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351 <has_text text="SQL ID" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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352 </assert_contents>
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353 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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diff changeset
354
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
355 <!-- samples -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
356 <output_collection name="tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
357 <element name="PopA_01.tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
358 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
359 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
360 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
361 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
362 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
363 <output_collection name="snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
364 <element name="PopA_01.snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
365 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
366 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
367 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
368 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
369 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
370 <output_collection name="alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
371 <element name="PopA_01.alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
372 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
373 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
374 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
375 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
376 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
377 <output_collection name="matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
378 <element name="PopA_01.matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
379 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
380 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
381 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
382 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
383 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
384 </test>
3
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
385
0
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
386 <test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
387 <param name="options_usage|rad_analysis_type" value="population"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
388 <param name="options_usage|individual_sample" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq,demultiplexed/PopA_03.1.fq,demultiplexed/PopA_04.1.fq,demultiplexed/PopB_01.1.fq,demultiplexed/PopB_02.1.fq,demultiplexed/PopB_03.1.fq,demultiplexed/PopB_04.1.fq" ftype="fastqsanger" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
389 <param name="options_usage|popmap" value="denovo_map/popmap.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
390 <output name="output_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
391 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
392 <has_text text="denovo_map.pl completed" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
393 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
394 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
395
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
396 <!-- catalog -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
397 <output name="catalogtags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
398 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
399 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
400 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
401 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
402 <output name="catalogsnps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
403 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
404 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
405 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
406 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
407 <output name="catalogalleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
408 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
409 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
410 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
411 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
412
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
413 <!-- populations -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
414 <output name="out_haplotypes">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
415 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
416 <has_text text="PopA_01" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
417 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
418 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
419 <output name="out_hapstats">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
420 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
421 <has_text text="Smoothed Gene Diversity" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
422 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
423 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
424 <output name="out_populations_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
425 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
426 <has_text text="populations version" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
427 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
428 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
429 <output name="out_sumstats_sum">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
430 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
431 <has_text text="Polymorphic Sites" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
432 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
433 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
434 <output name="out_sumstats">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
435 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
436 <has_text text="Smoothed Pi" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
437 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
438 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
439
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
440 <!-- samples -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
441 <output_collection name="tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
442 <element name="PopA_01.tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
443 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
444 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
445 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
446 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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447 </output_collection>
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448 <output_collection name="snps">
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449 <element name="PopA_01.snps">
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450 <assert_contents>
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451 <has_text text="generated on " />
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452 </assert_contents>
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453 </element>
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454 </output_collection>
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455 <output_collection name="alleles">
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456 <element name="PopA_01.alleles">
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457 <assert_contents>
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458 <has_text text="generated on " />
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459 </assert_contents>
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460 </element>
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461 </output_collection>
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462 <output_collection name="matches">
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463 <element name="PopA_01.matches">
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464 <assert_contents>
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465 <has_text text="generated on " />
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466 </assert_contents>
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467 </element>
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468 </output_collection>
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469 </test>
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470 </tests>
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471
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472 <help>
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473 <![CDATA[
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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474 .. class:: infomark
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475
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476 **What it does**
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477
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478 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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479
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480 --------
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481
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482 **Input files**
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483
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484 FASTQ, FASTA
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485
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486 - Population map::
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487
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488 indv_01 1
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489 indv_02 1
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490 indv_03 1
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491 indv_04 2
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492 indv_05 2
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493 indv_06 2
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494
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495
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496 **Output files**
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497
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498
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499 - XXX.tags.tsv file:
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500
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501 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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502
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503 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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504
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505
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506 - XXX.snps.tsv file:
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507
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508 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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509
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510 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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511
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512
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513 - XXX.alleles.tsv file:
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514
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515 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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516
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diff changeset
517
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518 - XXX.matches.tsv file:
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519
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520 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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diff changeset
521
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522 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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523
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524
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525 - other files:
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526
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527 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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diff changeset
528
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529 @STACKS_INFOS@
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530 ]]>
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531 </help>
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532 <expand macro="citation" />
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533 </tool>
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534