Mercurial > repos > iuc > stacks_refmap

annotate stacks_refmap.xml @ 9:f134c45859a8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 21:55:26 +0000
parents 0d516bfea0f2
children
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6fb6281a836f 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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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
9
f134c45859a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
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6 <expand macro="bio_tools"/>
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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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11 @CLEAN_EXT@
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12
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13 #if str( $options_usage.rad_analysis_type ) == "genetic"
ad7dd830f388 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
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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15 #if $input_parent.is_of_type('sam')
ad7dd830f388 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"
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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17 #else
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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
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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27 #if $input_progeny.is_of_type('sam')
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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28 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"
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29 #else
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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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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32
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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')
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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40 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"
ad7dd830f388 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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54
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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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69
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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"
0
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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"
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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)
0
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96 -m $m
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97 #end if
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98 #if str($P)
0
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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)." />
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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)." />
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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 argument="-m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" />
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155 <param argument="-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" />
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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" />
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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 ${on_string}">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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179 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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180 </collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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181
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182 <collection name="alleles" type="list" label="Haplotypes (alleles) recorded from each locus on ${on_string}">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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183 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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184 </collection>
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185
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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186 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
187 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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188 </collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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189
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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190 <collection name="all_output" type="list" label="Full output from ref_map on ${on_string}">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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191 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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192 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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193 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)$" ext="txt" directory="stacks_outputs" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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194 </collection>
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195 </outputs>
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196
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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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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iuc
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200 <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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201 <output name="output_log">
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iuc
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202 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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203 <has_text text="ref_map.pl completed" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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204 </assert_contents>
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205 </output>
5
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
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206 <output name="output_summary">
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iuc
parents: 2
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207 <assert_contents>
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iuc
parents: 2
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208 <has_text text="Stacks Statistics" />
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
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209 </assert_contents>
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iuc
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210 </output>
0
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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211
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
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212 <!-- catalog -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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213 <output name="catalogsnps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
214 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
215 <has_text text="catalog generated" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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216 </assert_contents>
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iuc
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diff changeset
217 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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218 <output name="catalogalleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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219 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
220 <has_text text="catalog generated" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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221 </assert_contents>
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iuc
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222 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
223 <output name="catalogtags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
224 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
225 <has_text text="catalog generated" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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226 </assert_contents>
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iuc
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diff changeset
227 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
228
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
229 <!-- genotypes -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
230 <output name="out_generic_haplo">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
231 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
232 <has_text text="Catalog ID" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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233 </assert_contents>
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iuc
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diff changeset
234 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
235 <output name="out_sql_markers">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
236 <assert_contents>
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iuc
parents:
diff changeset
237 <has_text text="Total Genotypes" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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238 </assert_contents>
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iuc
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diff changeset
239 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
240 <output name="out_joinmap">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
241 <assert_contents>
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iuc
parents:
diff changeset
242 <has_text text="batch_1.genotypes_" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
243 </assert_contents>
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iuc
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diff changeset
244 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
245 <output name="out_sql_genotypes">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
246 <assert_contents>
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iuc
parents:
diff changeset
247 <has_text text="SQL ID" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
248 </assert_contents>
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iuc
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diff changeset
249 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
250 <output name="out_generic_haplo">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
251 <assert_contents>
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iuc
parents:
diff changeset
252 <has_text text="Seg Dist" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
253 </assert_contents>
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iuc
parents:
diff changeset
254 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
255 <output name="out_sql_markers">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
256 <assert_contents>
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iuc
parents:
diff changeset
257 <has_text text="Total Genotypes" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
258 </assert_contents>
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iuc
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diff changeset
259 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
260
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
261 <!-- samples -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
262 <output_collection name="tags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
263 <element name="PopA_01.tags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
264 <assert_contents>
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iuc
parents:
diff changeset
265 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
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266 </assert_contents>
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iuc
parents:
diff changeset
267 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
268 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
269 <output_collection name="snps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
270 <element name="PopA_01.snps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
271 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
272 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
273 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
274 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
275 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
276 <output_collection name="alleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
277 <element name="PopA_01.alleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
278 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
279 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
280 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
281 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
282 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
283 <output_collection name="matches">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
284 <element name="PopA_01.matches">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
285 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
286 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
287 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
288 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
289 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
290 </test>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
291 <test>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
292 <param name="options_usage|rad_analysis_type" value="genetic"/>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
293 <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
294 <param name="options_usage|progeny_alignments" value="refmap/PopA_02.bam" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
295 <output name="output_log">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
296 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
297 <has_text text="ref_map.pl completed" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
298 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
299 </output>
5
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
300 <output name="output_summary">
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
301 <assert_contents>
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
302 <has_text text="Stacks Statistics" />
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
303 </assert_contents>
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
304 </output>
0
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
305
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
306 <!-- catalog -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
307 <output name="catalogsnps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
308 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
309 <has_text text="catalog generated" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
310 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
311 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
312 <output name="catalogalleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
313 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
314 <has_text text="catalog generated" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
315 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
316 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
317 <output name="catalogtags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
318 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
319 <has_text text="catalog generated" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
320 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
321 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
322
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
323 <!-- genotypes -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
324 <output name="out_generic_haplo">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
325 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
326 <has_text text="Catalog ID" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
327 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
328 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
329 <output name="out_sql_markers">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
330 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
331 <has_text text="Total Genotypes" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
332 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
333 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
334 <output name="out_joinmap">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
335 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
336 <has_text text="batch_1.genotypes_" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
337 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
338 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
339 <output name="out_sql_genotypes">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
340 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
341 <has_text text="SQL ID" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
342 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
343 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
344 <output name="out_generic_haplo">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
345 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
346 <has_text text="Seg Dist" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
347 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
348 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
349 <output name="out_sql_markers">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
350 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
351 <has_text text="Total Genotypes" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
352 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
353 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
354
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
355 <!-- samples -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
356 <output_collection name="tags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
357 <element name="PopA_01.tags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
358 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
359 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
360 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
361 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
362 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
363 <output_collection name="snps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
364 <element name="PopA_01.snps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
365 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
366 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
367 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
368 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
369 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
370 <output_collection name="alleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
371 <element name="PopA_01.alleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
372 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
373 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
374 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
375 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
376 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
377 <output_collection name="matches">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
378 <element name="PopA_01.matches">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
379 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
380 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
381 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
382 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
383 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
384 </test>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
385 <test>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
386 <param name="options_usage|rad_analysis_type" value="population"/>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
388 <param name="options_usage|popmap" value="denovo_map/popmap.tsv" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
389 <output name="output_log">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
390 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
391 <has_text text="ref_map.pl completed" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
392 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
393 </output>
5
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
394 <output name="output_summary">
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
395 <assert_contents>
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
396 <has_text text="Stacks Statistics" />
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
397 </assert_contents>
ad7dd830f388 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents: 2
diff changeset
398 </output>
0
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
399
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
400 <!-- catalog -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
401 <output name="catalogtags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
402 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
403 <has_text text="catalog generated on" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
404 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
405 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
406 <output name="catalogsnps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
407 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
408 <has_text text="catalog generated on" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
409 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
410 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
411 <output name="catalogalleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
412 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
413 <has_text text="catalog generated on" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
414 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
415 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
416
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
417 <!-- populations -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
418 <output name="out_haplotypes">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
419 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
420 <has_text text="PopA_01" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
421 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
422 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
423 <output name="out_hapstats">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
424 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
425 <has_text text="Smoothed Gene Diversity" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
426 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
427 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
428 <output name="out_populations_log">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
429 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
430 <has_text text="populations version" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
431 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
432 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
433 <output name="out_sumstats_sum">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
434 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
435 <has_text text="Polymorphic Sites" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
436 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
437 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
438 <output name="out_sumstats">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
439 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
440 <has_text text="Smoothed Pi" />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
441 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
442 </output>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
443
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
444 <!-- samples -->
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
445 <output_collection name="tags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
446 <element name="PopA_01.tags">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
447 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
448 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
449 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
450 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
451 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
452 <output_collection name="snps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
453 <element name="PopA_01.snps">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
454 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
455 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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456 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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457 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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458 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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459 <output_collection name="alleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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460 <element name="PopA_01.alleles">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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461 <assert_contents>
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462 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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463 </assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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464 </element>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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465 </output_collection>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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466 <output_collection name="matches">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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467 <element name="PopA_01.matches">
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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468 <assert_contents>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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469 <has_text text="generated on " />
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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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
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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476 <help>
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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477 <![CDATA[
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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478 .. class:: infomark
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479
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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480 **What it does**
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481
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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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
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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486 **Input files**
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487
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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488 - SAM, BAM
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489
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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490 - Population map::
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491
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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492 indv_01 1
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493 indv_02 1
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494 indv_03 1
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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
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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499 **Output files**
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500
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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501 - XXX.tags.tsv file:
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502
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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503 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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504
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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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
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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508 - XXX.snps.tsv file:
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509
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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510 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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511
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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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
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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514
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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515 - XXX.alleles.tsv file:
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516
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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517 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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518
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
519
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
520 - XXX.matches.tsv file:
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521
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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522 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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523
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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
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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526
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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527 - other files:
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528
457e01b31aa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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529 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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530
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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>