Mercurial > repos > iuc > stacks_denovomap

annotate stacks_denovomap.xml @ 2:b8827c571fbd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
author iuc
date Wed, 15 Jun 2016 06:24:47 -0400
parents 9d588fb2aee5
children bab631cc9f64
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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 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.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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14
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15 #if $input_parent.ext == "fastqsanger":
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16 #set $data_path = splitext($input_parent.name)[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.name)[0]
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21 #set $data_path = re.sub(r'\.1$', '', $data_path)
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22 #set $data_path = $data_path + ".fa"
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23 #end if
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24
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25 ln -s "${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
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30 #if $input_progeny.ext == "fastqsanger":
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31 #set $data_path = splitext($input_progeny.name)[0]
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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.name)[0]
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36 #set $data_path = re.sub(r'\.1$', '', $data_path)
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37 #set $data_path = $data_path + ".fa"
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38 #end if
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39
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40 ln -s "${input_progeny}" "${data_path}" &&
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41 #end for
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42 #else:
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43 #for $input_indiv in $options_usage.individual_sample:
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44
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45 #if $input_indiv.ext == "fastqsanger":
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46 #set $data_path = splitext($input_indiv.name)[0]
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47 #set $data_path = re.sub(r'\.1$', '', $data_path)
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48 #set $data_path = $data_path + ".fq"
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49 #else:
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50 #set $data_path = splitext($input_indiv.name)[0]
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51 #set $data_path = re.sub(r'\.1$', '', $data_path)
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52 #set $data_path = $data_path + ".fa"
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53 #end if
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54
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55 ln -s "${input_indiv}" "${data_path}" &&
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56 #end for
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57 #end if
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58
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59 mkdir stacks_outputs
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61 &&
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62
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63 denovo_map.pl
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64
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65 -T \${GALAXY_SLOTS:-1}
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66
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67 #if str( $options_usage.rad_analysis_type ) == "genetic":
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68 #for $input_parent in $options_usage.parent_sequences:
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69 #if $input_parent.ext == "fastqsanger":
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70 #set $data_path = splitext($input_parent.name)[0]
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71 #set $data_path = re.sub(r'\.1$', '', $data_path)
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72 #set $data_path = $data_path + ".fq"
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73 #else:
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74 #set $data_path = splitext($input_parent.name)[0]
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75 #set $data_path = re.sub(r'\.1$', '', $data_path)
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76 #set $data_path = $data_path + ".fa"
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77 #end if
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78
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79 -p "${data_path}"
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80 #end for
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81
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82 -A $options_usage.cross_type
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83
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84 #for $input_progeny in $options_usage.progeny_sequences:
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85 #if $input_progeny.ext == "fastqsanger":
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86 #set $data_path = splitext($input_progeny.name)[0]
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87 #set $data_path = re.sub(r'\.1$', '', $data_path)
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88 #set $data_path = $data_path + ".fq"
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89 #else:
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90 #set $data_path = splitext($input_progeny.name)[0]
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91 #set $data_path = re.sub(r'\.1$', '', $data_path)
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92 #set $data_path = $data_path + ".fa"
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93 #end if
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94
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95 -r "${data_path}"
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96 #end for
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97
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98 #if str($assembly_options.P):
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99 -P $assembly_options.P
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100 #end if
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101 #else:
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102 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample):
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103
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104 #if $input_indiv.ext == "fastqsanger":
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105 #set $data_path = splitext($input_indiv.name)[0]
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106 #set $data_path = re.sub(r'\.1$', '', $data_path)
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107 #set $data_path = $data_path + ".fq"
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108 #else:
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109 #set $data_path = splitext($input_indiv.name)[0]
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110 #set $data_path = re.sub(r'\.1$', '', $data_path)
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111 #set $data_path = $data_path + ".fa"
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112 #end if
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113
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114 -s "${data_path}"
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115 #end for
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116 -O "$options_usage.popmap"
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117 #end if
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118
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119 #if str($assembly_options.m):
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120 -m $assembly_options.m
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121 #end if
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122 #if str($assembly_options.N):
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123 -N $assembly_options.N
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124 #end if
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125 -M $assembly_options.M
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126 -n $assembly_options.n
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127 -t $assembly_options.t
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128 -H $assembly_options.H
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129
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130 ## Batch description
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131 -b 1
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132
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133 ## No SQL recording
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134 -S
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135
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136 ## snp_model
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137 #if str( $snp_options.select_model.model_type) == "bounded":
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138 --bound_low $snp_options.select_model.bound_low
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139 --bound_high $snp_options.select_model.bound_high
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140 --alpha $snp_options.select_model.alpha
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141 #else if str( $snp_options.select_model.model_type) == "snp":
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142 --alpha $snp_options.select_model.alpha
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143 #end if
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144
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145 -o stacks_outputs
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146
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147 #if str( $options_usage.rad_analysis_type ) == "genetic":
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148 @NORM_GENOTYPES_OUTPUT_LIGHT@
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149 #end if
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150 ]]></command>
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151
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152 <inputs>
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153 <conditional name="options_usage">
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154 <param name="rad_analysis_type" type="select" label="Select your usage">
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155 <option value="genetic" selected="true">Genetic map</option>
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156 <option value="population">Population</option>
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157 </param>
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158 <when value="genetic">
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159 <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" />
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160
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161 <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" />
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162
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163 <param name="cross_type" argument="-A" type="select" label="Cross type">
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164 <expand macro="cross_types"/>
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165 </param>
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166 </when>
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167 <when value="population">
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168 <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" />
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169 <param name="popmap" argument="-O" type="data" format="tabular,txt" label="Specify a population map" />
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170 </when>
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171 </conditional>
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172
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173 <!-- stack assembly options -->
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174 <section name="assembly_options" title="Assembly options" expanded="false">
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175 <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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176 <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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177 <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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178 <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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179 <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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180
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181 <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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182 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
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183 </section>
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184
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185 <!-- SNP Model options -->
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186 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
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187 <expand macro="snp_options"/>
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188 </section>
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189 </inputs>
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190 <outputs>
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191 <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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192
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193 <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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194 <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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195 <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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196
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197 <expand macro="genotypes_output_light"/>
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198 <expand macro="populations_output_light"/>
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199
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200 <collection name="tags" type="list" label="Assembled loci from ${on_string}">
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201 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" />
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202 </collection>
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203
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204 <collection name="snps" type="list" label="Model calls from each locus on ${on_string}">
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205 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />
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206 </collection>
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207
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208 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}">
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209 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" />
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210 </collection>
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211
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212 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
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213 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv" ext="tabular" directory="stacks_outputs" />
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214 </collection>
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215
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216 <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}">
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217 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv" ext="tabular" directory="stacks_outputs" />
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218 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv" ext="tabular" directory="stacks_outputs" />
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219 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)" ext="txt" directory="stacks_outputs" />
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220 </collection>
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221 </outputs>
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222
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223 <tests>
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224 <test>
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225 <param name="options_usage|rad_analysis_type" value="genetic"/>
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226 <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
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227 <param name="options_usage|progeny_sequences" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
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228 <output name="output_log">
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229 <assert_contents>
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230 <has_text text="denovo_map.pl completed" />
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231 </assert_contents>
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232 </output>
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233
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234 <!-- catalog -->
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235 <output name="catalogtags">
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236 <assert_contents>
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237 <has_text text="catalog generated on" />
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238 </assert_contents>
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239 </output>
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240 <output name="catalogsnps">
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241 <assert_contents>
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242 <has_text text="catalog generated on" />
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243 </assert_contents>
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244 </output>
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245 <output name="catalogalleles">
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246 <assert_contents>
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247 <has_text text="catalog generated on" />
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248 </assert_contents>
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249 </output>
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250
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251 <!-- genotypes -->
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252 <output name="out_generic_haplo">
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253 <assert_contents>
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254 <has_text text="Catalog ID" />
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255 </assert_contents>
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256 </output>
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257 <output name="out_sql_markers">
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258 <assert_contents>
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259 <has_text text="Total Genotypes" />
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260 </assert_contents>
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261 </output>
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262 <output name="out_joinmap">
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263 <assert_contents>
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264 <has_text text="batch_1.genotypes_" />
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265 </assert_contents>
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266 </output>
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iuc
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267 <output name="out_sql_genotypes">
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268 <assert_contents>
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iuc
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269 <has_text text="SQL ID" />
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270 </assert_contents>
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271 </output>
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272
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273 <!-- samples -->
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iuc
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diff changeset
274 <output_collection name="tags">
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iuc
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275 <element name="PopA_01.tags">
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iuc
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276 <assert_contents>
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iuc
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277 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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278 </assert_contents>
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279 </element>
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280 </output_collection>
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iuc
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281 <output_collection name="snps">
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iuc
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282 <element name="PopA_01.snps">
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iuc
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283 <assert_contents>
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iuc
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284 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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285 </assert_contents>
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286 </element>
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287 </output_collection>
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iuc
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288 <output_collection name="alleles">
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iuc
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289 <element name="PopA_01.alleles">
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iuc
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290 <assert_contents>
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iuc
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291 <has_text text="generated on " />
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292 </assert_contents>
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293 </element>
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294 </output_collection>
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iuc
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295 <output_collection name="matches">
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iuc
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diff changeset
296 <element name="PopA_01.matches">
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iuc
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297 <assert_contents>
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iuc
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298 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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299 </assert_contents>
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iuc
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diff changeset
300 </element>
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301 </output_collection>
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iuc
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302 </test>
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iuc
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diff changeset
303 <test>
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304 <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
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305 <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
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306 <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
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diff changeset
307 <output name="output_log">
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iuc
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308 <assert_contents>
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iuc
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309 <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
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310 </assert_contents>
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iuc
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311 </output>
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iuc
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diff changeset
312
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
313 <!-- catalog -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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314 <output name="catalogtags">
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iuc
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315 <assert_contents>
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iuc
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diff changeset
316 <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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317 </assert_contents>
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iuc
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318 </output>
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iuc
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diff changeset
319 <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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diff changeset
320 <assert_contents>
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iuc
parents:
diff changeset
321 <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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322 </assert_contents>
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iuc
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diff changeset
323 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
324 <output name="catalogalleles">
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iuc
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diff changeset
325 <assert_contents>
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iuc
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diff changeset
326 <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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327 </assert_contents>
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iuc
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328 </output>
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iuc
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diff changeset
329
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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330 <!-- populations -->
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iuc
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331 <output name="out_haplotypes">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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332 <assert_contents>
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iuc
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333 <has_text text="PopA_01" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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334 </assert_contents>
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335 </output>
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iuc
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336 <output name="out_hapstats">
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iuc
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337 <assert_contents>
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iuc
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338 <has_text text="Smoothed Gene Diversity" />
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339 </assert_contents>
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iuc
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340 </output>
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iuc
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341 <output name="out_populations_log">
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iuc
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342 <assert_contents>
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iuc
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343 <has_text text="populations version" />
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344 </assert_contents>
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345 </output>
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iuc
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diff changeset
346 <output name="out_sumstats_sum">
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iuc
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diff changeset
347 <assert_contents>
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iuc
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348 <has_text text="Polymorphic Sites" />
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iuc
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349 </assert_contents>
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iuc
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350 </output>
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iuc
parents:
diff changeset
351 <output name="out_sumstats">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
352 <assert_contents>
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iuc
parents:
diff changeset
353 <has_text text="Smoothed Pi" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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354 </assert_contents>
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iuc
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diff changeset
355 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
356
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357 <!-- samples -->
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358 <output_collection name="tags">
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359 <element name="PopA_01.tags">
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360 <assert_contents>
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361 <has_text text="generated on " />
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362 </assert_contents>
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363 </element>
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364 </output_collection>
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365 <output_collection name="snps">
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366 <element name="PopA_01.snps">
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367 <assert_contents>
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368 <has_text text="generated on " />
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369 </assert_contents>
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370 </element>
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371 </output_collection>
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372 <output_collection name="alleles">
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373 <element name="PopA_01.alleles">
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374 <assert_contents>
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375 <has_text text="generated on " />
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376 </assert_contents>
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377 </element>
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378 </output_collection>
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379 <output_collection name="matches">
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380 <element name="PopA_01.matches">
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381 <assert_contents>
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382 <has_text text="generated on " />
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383 </assert_contents>
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384 </element>
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385 </output_collection>
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386 </test>
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387 </tests>
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388
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389 <help>
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390 <![CDATA[
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391 .. class:: infomark
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392
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393 **What it does**
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394
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395 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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396
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397 --------
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398
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399 **Input files**
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400
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401 FASTQ, FASTA
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402
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403 - Population map::
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404
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405 indv_01 1
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406 indv_02 1
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407 indv_03 1
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408 indv_04 2
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409 indv_05 2
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410 indv_06 2
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411
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412
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413 **Output files**
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414
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415
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416 - XXX.tags.tsv file:
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417
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418 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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419
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420 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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421
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422
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423 - XXX.snps.tsv file:
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424
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425 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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426
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427 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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428
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429
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430 - XXX.alleles.tsv file:
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431
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432 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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433
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434
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435 - XXX.matches.tsv file:
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436
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437 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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438
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439 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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440
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441
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442 - other files:
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443
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444 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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445
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446 @STACKS_INFOS@
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447 ]]>
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448 </help>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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449 <expand macro="citation" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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450 </tool>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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451