Mercurial > repos > iuc > stacks_refmap

annotate stacks_refmap.xml @ 11:1ba1185929c1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
author iuc
date Tue, 22 Mar 2022 23:18:13 +0000
parents c209e3f3359b
children d7a482f44e08
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827c8c6ec4c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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1 <tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">
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2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
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1ba1185929c1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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11 @CLEAN_EXT@
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12
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13 #if str( $options_usage.rad_analysis_type ) == "genetic"
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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14 #for $input_parent in $options_usage.parent_alignments
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15 #if $input_parent.is_of_type('sam')
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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16 #set $data_path = $clean_ext($input_parent.element_identifier) + ".sam"
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17 #else
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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18 #set $data_path = $clean_ext($input_parent.element_identifier) + ".bam"
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19 #end if
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21 ln -s '${input_parent}' '${data_path}' &&
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22 #end for
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24 #for $input_progeny in $options_usage.progeny_alignments
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26 #if $input_progeny
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27 #if $input_progeny.is_of_type('sam')
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28 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"
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29 #else
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30 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".bam"
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31 #end if
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33 ln -s '${input_progeny}' '${data_path}' &&
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34 #end if
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35 #end for
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36 #else
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37 #for $input_indiv in $options_usage.individual_sample
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38
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39 #if $input_indiv.is_of_type('sam')
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40 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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41 #else
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42 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".bam"
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43 #end if
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44
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45 ln -s '${input_indiv}' '${data_path}' &&
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46 #end for
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47 #end if
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49 mkdir stacks_outputs
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51 &&
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53 ref_map.pl
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55 -T \${GALAXY_SLOTS:-1}
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56
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57 #if str( $options_usage.rad_analysis_type ) == "genetic"
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58 #for $input_parent in $options_usage.parent_alignments
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59 #if $input_parent.is_of_type('sam')
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60 #set $data_path = $clean_ext($input_parent.element_identifier) + ".sam"
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61 #else
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62 #set $data_path = $clean_ext($input_parent.element_identifier) + ".bam"
0
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63 #end if
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64
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65 -p '${data_path}'
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66 #end for
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67
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68 -A $options_usage.cross_type
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70 #for $input_progeny in $options_usage.progeny_alignments
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71 #if $input_progeny
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72 #if $input_progeny.is_of_type('sam')
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73 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"
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74 #else
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75 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".bam"
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76 #end if
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77
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78 -r '${data_path}'
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79 #end if
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80 #end for
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81 #else
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82 #for $input_indiv in $options_usage.individual_sample
0
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83
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84 #if $input_indiv.is_of_type('sam')
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85 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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86 #else
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87 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".bam"
0
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88 #end if
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89
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90 -s '${data_path}'
0
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91 #end for
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92 -O '$options_usage.popmap'
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93 #end if
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94
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95 #if str($m)
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96 -m $m
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97 #end if
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98 #if str($P)
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99 -P $P
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100 #end if
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101
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102 ## Batch description
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103 -b 1
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104
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105 ## No SQL recording
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106 -S
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107
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108 ## snp_model
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109 #if str( $snp_options.select_model.model_type) == "bounded"
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110 --bound_low $snp_options.select_model.bound_low
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111 --bound_high $snp_options.select_model.bound_high
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112 --alpha $snp_options.select_model.alpha
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113 #else if str( $snp_options.select_model.model_type) == "snp"
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114 --alpha $snp_options.select_model.alpha
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115 #end if
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116
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117 -o stacks_outputs
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118
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119 #if str( $options_usage.rad_analysis_type ) == "genetic"
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120 @NORM_GENOTYPES_OUTPUT_LIGHT@
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121 #end if
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122
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123 ## If input is in bam format, stacks will output gzipped files (no option to control this)
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124 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
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125
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126 &&
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127
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128 stacks_summary.py --stacks-prog ref_map.pl --res-dir stacks_outputs --logfile stacks_outputs/ref_map.log --summary stacks_outputs/summary.html
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129 #if str( $options_usage.rad_analysis_type ) == "population":
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130 --pop-map '$options_usage.popmap'
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131 #end if
0
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132 ]]></command>
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133
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134 <inputs>
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135 <conditional name="options_usage">
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136 <param name="rad_analysis_type" type="select" label="Select your usage">
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137 <option value="genetic" selected="true">Genetic map</option>
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138 <option value="population">Population</option>
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139 </param>
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140 <when value="genetic">
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141 <param name="parent_alignments" format="sam,bam" type="data" multiple="true" label="Files containing parent alignments" argument="-p" help="Dataset names will be used as sample name (no space allowed)." />
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142 <param name="progeny_alignments" format="sam,bam" type="data" multiple="true" optional="true" label="Files containing progeny alignments" argument="-r" help="Dataset names will be used as sample name (no space allowed)." />
0
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143
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144 <param name="cross_type" argument="-A" type="select" label="Cross type">
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145 <expand macro="cross_types"/>
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146 </param>
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147 </when>
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148 <when value="population">
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149 <param name="individual_sample" format="sam,bam" type="data" multiple="true" label="Files containing an individual sample from a population" argument="-s" help="Dataset names will be used as sample name (no space allowed)." />
0
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150 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-O" />
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151 </when>
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152 </conditional>
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153
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154 <param name="m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" argument="-m" />
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155 <param name="P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" argument="-P" />
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156
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157 <!-- SNP Model options -->
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158 <section name="snp_options" title="SNP_Model_Options" expanded="False">
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159 <expand macro="snp_options"/>
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160 </section>
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161 </inputs>
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162 <outputs>
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163 <data format="txt" name="output_log" label="ref_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/ref_map.log" />
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164
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165 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
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166
0
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167 <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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168 <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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169 <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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170
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171 <expand macro="genotypes_output_light"/>
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172 <expand macro="populations_output_light"/>
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173
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174 <collection name="tags" type="list" label="Assembled loci (tags) from ${on_string}">
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175 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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176 </collection>
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177
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178 <collection name="snps" type="list" label="Model calls (snps) from each locus on ${on_string}">
3
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179 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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180 </collection>
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181
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182 <collection name="alleles" type="list" label="Haplotypes (alleles) recorded from each locus on ${on_string}">
3
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183 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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184 </collection>
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185
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186 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
3
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187 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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188 </collection>
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189
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190 <collection name="all_output" type="list" label="Full output from ref_map on ${on_string}">
3
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191 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" />
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192 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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193 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)$" ext="txt" directory="stacks_outputs" />
0
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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194 </collection>
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195 </outputs>
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196
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197 <tests>
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198 <test>
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199 <param name="options_usage|rad_analysis_type" value="genetic"/>
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200 <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />
3
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201 <output name="output_log">
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202 <assert_contents>
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203 <has_text text="ref_map.pl completed" />
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204 </assert_contents>
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205 </output>
8
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206 <output name="output_summary">
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207 <assert_contents>
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208 <has_text text="Stacks Statistics" />
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209 </assert_contents>
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210 </output>
3
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211
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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212 <!-- catalog -->
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213 <output name="catalogsnps">
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214 <assert_contents>
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215 <has_text text="catalog generated" />
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216 </assert_contents>
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217 </output>
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218 <output name="catalogalleles">
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219 <assert_contents>
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220 <has_text text="catalog generated" />
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221 </assert_contents>
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222 </output>
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223 <output name="catalogtags">
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224 <assert_contents>
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225 <has_text text="catalog generated" />
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226 </assert_contents>
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227 </output>
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228
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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229 <!-- genotypes -->
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230 <output name="out_generic_haplo">
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231 <assert_contents>
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232 <has_text text="Catalog ID" />
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233 </assert_contents>
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234 </output>
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235 <output name="out_sql_markers">
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236 <assert_contents>
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237 <has_text text="Total Genotypes" />
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238 </assert_contents>
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239 </output>
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240 <output name="out_joinmap">
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241 <assert_contents>
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242 <has_text text="batch_1.genotypes_" />
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243 </assert_contents>
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244 </output>
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245 <output name="out_sql_genotypes">
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246 <assert_contents>
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247 <has_text text="SQL ID" />
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248 </assert_contents>
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249 </output>
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250 <output name="out_generic_haplo">
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251 <assert_contents>
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252 <has_text text="Seg Dist" />
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253 </assert_contents>
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254 </output>
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255 <output name="out_sql_markers">
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256 <assert_contents>
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257 <has_text text="Total Genotypes" />
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258 </assert_contents>
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259 </output>
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260
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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261 <!-- samples -->
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262 <output_collection name="tags">
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263 <element name="PopA_01.tags">
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264 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
265 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
266 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
267 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
268 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
269 <output_collection name="snps">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
270 <element name="PopA_01.snps">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
271 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
272 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
273 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
274 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
275 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
276 <output_collection name="alleles">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
277 <element name="PopA_01.alleles">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
278 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
279 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
280 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
281 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
282 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
283 <output_collection name="matches">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
284 <element name="PopA_01.matches">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
285 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
286 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
287 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
288 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
289 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
290 </test>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
291 <test>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
292 <param name="options_usage|rad_analysis_type" value="genetic"/>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
293 <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />
0
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
294 <param name="options_usage|progeny_alignments" value="refmap/PopA_02.bam" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
295 <output name="output_log">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
296 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
297 <has_text text="ref_map.pl completed" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
298 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
299 </output>
8
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
300 <output name="output_summary">
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
301 <assert_contents>
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
302 <has_text text="Stacks Statistics" />
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
303 </assert_contents>
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
304 </output>
0
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
305
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
306 <!-- catalog -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
307 <output name="catalogsnps">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
308 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
309 <has_text text="catalog generated" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
310 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
311 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
312 <output name="catalogalleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
313 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
314 <has_text text="catalog generated" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
315 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
316 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
317 <output name="catalogtags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
318 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
319 <has_text text="catalog generated" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
320 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
321 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
322
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
323 <!-- genotypes -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
324 <output name="out_generic_haplo">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
325 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
326 <has_text text="Catalog ID" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
327 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
328 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
329 <output name="out_sql_markers">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
330 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
331 <has_text text="Total Genotypes" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
332 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
333 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
334 <output name="out_joinmap">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
335 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
336 <has_text text="batch_1.genotypes_" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
337 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
338 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
339 <output name="out_sql_genotypes">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
340 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
341 <has_text text="SQL ID" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
342 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
343 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
344 <output name="out_generic_haplo">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
345 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
346 <has_text text="Seg Dist" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
347 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
348 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
349 <output name="out_sql_markers">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
350 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
351 <has_text text="Total Genotypes" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
352 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
353 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
354
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
355 <!-- samples -->
66d3c1ae3937 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">
66d3c1ae3937 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">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
358 <assert_contents>
66d3c1ae3937 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 " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
360 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
361 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
362 </output_collection>
66d3c1ae3937 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">
66d3c1ae3937 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">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
365 <assert_contents>
66d3c1ae3937 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 " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
367 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
368 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
369 </output_collection>
66d3c1ae3937 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">
66d3c1ae3937 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">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
372 <assert_contents>
66d3c1ae3937 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 " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
374 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
375 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
376 </output_collection>
66d3c1ae3937 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">
66d3c1ae3937 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">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
379 <assert_contents>
66d3c1ae3937 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 " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
381 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
382 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
383 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
384 </test>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
385 <test>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
386 <param name="options_usage|rad_analysis_type" value="population"/>
66d3c1ae3937 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|individual_sample" value="refmap/PopA_01.bam,refmap/PopA_02.bam,refmap/PopA_03.bam,refmap/PopA_04.bam,refmap/PopB_01.bam,refmap/PopB_02.bam,refmap/PopB_03.bam,refmap/PopB_04.bam" />
66d3c1ae3937 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|popmap" value="denovo_map/popmap.tsv" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
389 <output name="output_log">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
390 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
391 <has_text text="ref_map.pl completed" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
392 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
393 </output>
8
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
394 <output name="output_summary">
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
395 <assert_contents>
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
396 <has_text text="Stacks Statistics" />
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
397 </assert_contents>
c209e3f3359b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 5
diff changeset
398 </output>
0
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
399
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
400 <!-- catalog -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
401 <output name="catalogtags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
402 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
403 <has_text text="catalog generated on" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
404 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
405 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
406 <output name="catalogsnps">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
407 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
408 <has_text text="catalog generated on" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
409 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
410 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
411 <output name="catalogalleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
412 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
413 <has_text text="catalog generated on" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
414 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
415 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
416
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
417 <!-- populations -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
418 <output name="out_haplotypes">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
419 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
420 <has_text text="PopA_01" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
421 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
422 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
423 <output name="out_hapstats">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
424 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
425 <has_text text="Smoothed Gene Diversity" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
426 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
427 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
428 <output name="out_populations_log">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
429 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
430 <has_text text="populations version" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
431 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
432 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
433 <output name="out_sumstats_sum">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
434 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
435 <has_text text="Polymorphic Sites" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
436 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
437 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
438 <output name="out_sumstats">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
439 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
440 <has_text text="Smoothed Pi" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
441 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
442 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
443
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
444 <!-- samples -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
445 <output_collection name="tags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
446 <element name="PopA_01.tags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
447 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
448 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
449 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
450 </element>
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451 </output_collection>
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452 <output_collection name="snps">
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453 <element name="PopA_01.snps">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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454 <assert_contents>
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455 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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456 </assert_contents>
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457 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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458 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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diff changeset
459 <output_collection name="alleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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460 <element name="PopA_01.alleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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461 <assert_contents>
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462 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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463 </assert_contents>
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464 </element>
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465 </output_collection>
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466 <output_collection name="matches">
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467 <element name="PopA_01.matches">
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468 <assert_contents>
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469 <has_text text="generated on " />
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470 </assert_contents>
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471 </element>
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472 </output_collection>
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473 </test>
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474 </tests>
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475
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476 <help>
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477 <![CDATA[
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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478 .. class:: infomark
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479
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480 **What it does**
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481
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482 This program expects data that have been aligned to a reference genome, and can accept data directly from Bowtie, or from any aligner that can produce SAM format. To avoid datasets names problems, we recommand the use of the *Map with BWA for STACKS tool*. This program will execute each of the Stacks components: first, running pstacks on each of the samples specified, building loci (based on the reference alignment) and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci specified as 'parents' or 'samples' on the command line, again using alignment to match loci in the catalog. Finally, sstacks will be executed to match each sample against the catalog. The ref_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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483
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484 --------
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485
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486 **Input files**
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487
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488 - SAM, BAM
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489
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490 - Population map::
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491
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492 indv_01 1
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493 indv_02 1
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494 indv_03 1
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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495 indv_04 2
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496 indv_05 2
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497 indv_06 2
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498
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499 **Output files**
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500
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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501 - XXX.tags.tsv file:
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502
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503 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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504
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505 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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506
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507
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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508 - XXX.snps.tsv file:
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509
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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510 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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diff changeset
511
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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512 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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513
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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514
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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515 - XXX.alleles.tsv file:
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516
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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517 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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518
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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diff changeset
519
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diff changeset
520 - XXX.matches.tsv file:
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diff changeset
521
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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522 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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diff changeset
523
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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524 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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525
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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526
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527 - other files:
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528
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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529 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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diff changeset
530
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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diff changeset
531 @STACKS_INFOS@
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532 ]]>
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533 </help>
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534 <expand macro="citation" />
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535 </tool>