Mercurial > repos > matthias > stacks2_populations

annotate stacks_populations.xml @ 4:cc87f9d30171 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
author matthias
date Fri, 04 Jan 2019 03:37:16 -0500
parents d530aff416bd
children 35e673d79262
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1 <tool id="stacks2_populations" name="Stacks2: populations" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>analyze a population of individual samples ('populations' program)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command><![CDATA[
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9 #import re
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10
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11 mkdir stacks_inputs stacks_outputs
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12
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13 &&
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14
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15 #if str($options_usage.input_type) == 'stacks'
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16 #for $input_file in $options_usage.input_aln
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17 #set $filename = str($input_file.element_identifier)
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18 #if $filename == "catalog.calls" or $filename == "catalog.fa.gz":
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19 ln -s '${input_file}' 'stacks_inputs/${filename}' &&
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20 #elif $filename == "catalog.calls.vcf":
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21 gzip -c '${input_file}' > stacks_inputs/catalog.calls &&
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22 #end if
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23 #end for
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24 #else if str($options_usage.input_type) == 'vcf'
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25 ln -s '$options_usage.input_vcf' 'stacks_inputs/input.vcf' &&
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26 #end if
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27
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28 populations
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29
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30 -t \${GALAXY_SLOTS:-1}
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31
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32 #if str($options_usage.input_type) == 'vcf'
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33 -V stacks_inputs/input.vcf
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34 #else
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35 -P stacks_inputs
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36 #end if
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37 -O stacks_outputs
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38
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39 #if str($popmap) != 'None':
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40 -M '$popmap'
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41 #end if
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42 #if str($batch_size) != '':
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43 -batch_size '$batch_size'
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44 #end if
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45
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46 ## Data filtering
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47
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48 -p $options_filtering.minpop
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49 -r $options_filtering.minperc
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50 --min_maf $options_filtering.minminor
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51 --min_mac $options_filtering.min_mac
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52 #if str($options_filtering.max_obs_het)
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53 --max_obs_het $options_filtering.max_obs_het
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54 #end if
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55 ## deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
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56 ## #if str($options_filtering.lnl)
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57 ## --lnl_lim $options_filtering.lnl
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58 ## #end if
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59 $options_filtering.filter_single_snp
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60 #if $options_filtering.blacklist
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61 -B '$options_filtering.blacklist'
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62 #end if
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63 #if $options_filtering.whitelist
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64 -W '$options_filtering.whitelist'
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65 #end if
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66
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67 ## Merging and Phasing:
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68 #if str($merge_phase.enzyme) != '':
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69 -e $merge_phase.enzyme
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70 #end if
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71 $merge_phase.merge_sites
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72 --merge_prune_lim $merge_phase.merge_prune_lim
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73
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74 ## Locus stats:
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75 $locus_stats.hwe
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76
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77 ## Fstats
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78 #if str($fstats_conditional.fstats) != 'no':
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79 --fstats
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80 #if str( $fstats_conditional.correction_select.correction ) != "no_corr"
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81 --fst_correction $fstats_conditional.correction_select.correction
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82 --p_value_cutoff $fstats_conditional.correction_select.pcutoff
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83 #end if
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84 #end if
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85
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86 ## Kernel-smoothing algorithm:
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87 $kernel_smoothing.options_kernel.kernel
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88 #if str($kernel_smoothing.options_kernel.kernel)!='':
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89 --sigma $kernel_smoothing.options_kernel.sigma
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90 #end if
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91 #if $kernel_smoothing.bootstrap_resampling_mode.bootstrap_all
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92 --bootstrap
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93 #else
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94 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_pifis
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95 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_fst
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96 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_div
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97 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist
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98 #end if
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99
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100 #if $kernel_smoothing.bootstrap_resampling_mode.bootstrap_all or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_pifis or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_fst or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_div or $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist:
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101 #if str($kernel_smoothing.bootstrap_reps)
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102 --bootstrap_reps $kernel_smoothing.bootstrap_reps
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103 #end if
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104 #if $kernel_smoothing.bootstrap_wl
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105 --bootstrap_wl '$kernel_smoothing.bootstrap_wl'
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106 #end if
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107 #end if
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108
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109 ## File output options:
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110
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111 $populations_output.ordered_export
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112 $populations_output.fasta_loci
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113 $populations_output.fasta_samples
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114 $populations_output.vcf
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115 $populations_output.genepop
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116 $populations_output.structure
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117 $populations_output.radpainter
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118 ##$populations_output.phase
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119 ##$populations_output.fastphase
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120 $populations_output.plink
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121 ##$populations_output.hzar
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122 $populations_output.phylip
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123 $populations_output.phylip_var
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124 ##$populations_output.phylip_var_all
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125 ##$populations_output.treemix
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126 $populations_output.no_hap_exports
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127 $populations_output.fasta_samples_raw
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128
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129 ## Additional options:
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130
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131 $advanced_options.log_fst_comp
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132
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133 ## populations outputs log info to stdout for vcf input
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134 ## for gstacks input it creates stacks_output/population.log
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135 ## in the latter case we take the log file
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136 ## also for vcf input the output files are named input.p....
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137 ## instead of populations...
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138
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139 #if str($options_usage.input_type) == 'vcf'
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140 > $output_log
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141 && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done
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142 #else
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143 && mv stacks_outputs/populations.log $output_log
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144 #end if
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145 ]]></command>
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146
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147 <inputs>
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148 <conditional name="options_usage">
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149 <param name="input_type" type="select" label="Input type" help="select input file type" >
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150 <option value="stacks">Stacks output</option>
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151 <option value="vcf">VCF file</option>
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152 </param>
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153 <when value="stacks">
4
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154 <expand macro="input_aln_macro"/>
0
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155 </when>
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156 <when value="vcf">
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157 <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" />
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158 </when>
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159 </conditional>
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160 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" help="Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'." optional="true"/>
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161 <param argument="--batch_size" type="integer" value="" optional="true" label="number of loci to process in a batch" help="(default: 10,000 in de novo mode; in reference mode, one chromosome per batch). Increase to speed analysis, uses more memory, decrease to save memory)"/>
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162
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163 <!-- Data Filtering -->
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164 <section name="options_filtering" title="Data filtering options" expanded="true">
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165
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166 <param name="minperc" argument="-r" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" />
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167 <param name="minpop" argument="-p" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus" />
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168 <param name="minminor" argument="--min_maf" type="float" value="0" min="0" max="0.5" label="minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus" />
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169 <param argument="--min_mac" type="integer" value="0" min="0" label="minimum minor allele count" help="specify a minimum minor allele count required to process a nucleotide site at a locus" />
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170 <param argument="--max_obs_het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus." />
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171 <!-- deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
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172 <param name="lnl" type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold" />-->
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173 <param name="filter_single_snp" type="select" label="Analyse all SNPs per locus" >
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174 <option value="">yes</option>
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175 <option value="--write_single_snp">No: Analyse only the first SNP (--write_single_snp)</option>
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176 <option value="--write_random_snp">No: Analyse only one random SNP (--write_random_snp)</option>
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177 </param>
3
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178 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export" />
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179 <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export" />
0
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180 </section>
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181
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182 <!-- merging and Phasing -->
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183 <section name="merge_phase" title="Merging and Phasing" expanded="true">
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184 <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" >
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185 <expand macro="enzymes"/>
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186 </param>
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187 <param argument="--merge_sites" truevalue="--merge_sites" falsevalue="" type="boolean" checked="false" label="merge loci that were produced from the same restriction enzyme cutsite" help="(requires reference-aligned data)" />
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188 <param argument="--merge_prune_lim" type="float" value="1.0" min="0.0" max="1.0" label="for merging adjacent loci: fraction of samples possessing both loci to prune remaining samples from analysis" />
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189 </section>
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190
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191 <!-- Locus stats -->
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192 <section name="locus_stats" title="Locus Stats" expanded="true">
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193 <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="calculate divergence from Hardy-Weinberg equilibrium for each locus" />
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194 </section>
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195
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196 <!-- Fstats -->
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197 <conditional name="fstats_conditional">
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198 <param name="fstats" argument="--fstats" type="select" label="Enable SNP and haplotype-based F statistics" >
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199 <option value="no">No</option>
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200 <option value="yes">Yes</option>
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201 </param>
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202 <when value="no"/>
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203 <when value="yes">
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204 <conditional name="correction_select">
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205 <param name="correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values" >
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206 <option value="no_corr">No correction</option>
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207 <option value="p_value">p_value</option>
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208 <option value="bonferroni_win">bonferroni_win</option>
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209 <option value="bonferroni_gen">bonferroni_gen</option>
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210 </param>
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211 <when value="no_corr"/>
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212 <when value="p_value">
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213 <param name="pcutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
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214 </when>
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215 <when value="bonferroni_win">
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216 <param name="pcutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
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217 </when>
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218 <when value="bonferroni_gen">
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219 <param name="pcutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" />
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220 </when>
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221 </conditional>
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222 </when>
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223 </conditional>
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224
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225 <!-- File output options -->
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226 <section name="populations_output" title="Output options" expanded="true">
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227 <param name="ordered_export" argument="--ordered_export" truevalue="--ordered_export" falsevalue="" type="boolean" checked="false" label="If data is reference aligned, exports will be ordered; only a single representative of each overlapping site." />
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228 <param name="fasta_loci" argument="--fasta_loci" truevalue="--fasta_loci" falsevalue="" type="boolean" checked="false" label="output locus consensus sequences in FASTA format" />
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229 <param name="fasta_samples" argument="--fasta_samples" truevalue="--fasta_samples" falsevalue="" type="boolean" checked="false" label="output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format" />
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230 <param name="vcf" argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" />
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231 <param name="genepop" argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" />
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232 <param name="structure" argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" />
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233 <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="output results in fineRADstructure/RADpainter format" />
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234 <!--<param name="phase" argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" />-->
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235 <param name="fastphase" argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" />
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236 <param name="plink" argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" />
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237 <!--<param name="hzar" argument="\-\-hzar" truevalue="\-\-hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." />-->
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238 <param name="phylip" argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction" />
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239 <param name="phylip_var" argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." />
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240 <!--<param name="phylip_var_all" argument="\-\-phylip_var_all" truevalue="\-\-phylip_var_all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation." />
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241 <param name="treemix" argument="\-\-treemix" truevalue="\-\-treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)." />-->
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242 <param argument="--no_hap_exports" truevalue="--no_hap_exports" falsevalue="" type="boolean" checked="false" label="omit haplotype outputs" />
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243 <param argument="--fasta_samples_raw" truevalue="--fasta_samples_raw" falsevalue="" type="boolean" checked="false" label="output all haplotypes observed in each sample, for each locus, in FASTA format" />
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244 </section>
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245
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246 <!-- Kernel-smoothing algorithm -->
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247 <section name="kernel_smoothing" title="Kernel smoothing" expanded="false">
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248 <conditional name="options_kernel">
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249 <param name="kernel" type="select" label="enable kernel-smoothed calculations" >
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250 <option value="">No</option>
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251 <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st</option>
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252 <option value="--smooth_fstats">For Fst, Fst', and Phi_st</option>
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253 <option value="--smooth_popstats">For Pi and Fis</option>
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254 </param>
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255 <when value=""/>
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256 <when value="-k">
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257 <param argument="--sigma" type="float" value="150000" label="standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" />
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258 </when>
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259 <when value="--smooth_fstats">
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260 <param argument="--sigma" type="float" value="150000" label="standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" />
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261 </when>
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262 <when value="--smooth_popstats">
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263 <param argument="--sigma" type="float" value="150000" label="standard deviation of the kernel smoothing weight distribution" help="distance over which to average values (default 150Kb)" />
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264 </when>
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265 </conditional>
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266 <conditional name="bootstrap_resampling_mode">
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267 <param name="bootstrap_all" argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics" >
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268 <option value="">No</option>
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269 <option value="--bootstrap">Yes</option>
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270 </param>
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271 <when value="--bootstrap">
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272 </when>
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273 <when value="">
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274 <param name="bootstrap_pifis" argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" />
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275 <param name="bootstrap_fst" argument="--bootstrap_fst" type="boolean" checked="false" truevalue="--bootstrap_fst" falsevalue="" label="Enable boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs" />
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276 <param name="bootstrap_div" argument="--bootstrap_div" type="boolean" checked="false" truevalue="--bootstrap_div" falsevalue="" label="Enable boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes" />
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277 <param name="bootstrap_phist" argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." />
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278 </when>
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279 </conditional>
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280 <param name="bootstrap_reps" argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" />
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281 <param name="bootstrap_wl" argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" />
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282 </section>
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283
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284 <!-- Output options -->
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285 <section name="advanced_options" title="Advanced options" expanded="False">
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286 <param argument="--log_fst_comp" type="boolean" checked="false" truevalue="--log_fst_comp" falsevalue="" label="log components of Fst/Phi_st calculations to a data set" />
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287 </section>
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288 <expand macro="in_log"/>
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289 </inputs>
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290 <outputs>
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291 <expand macro="out_log"/>
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292 <expand macro="populations_output_full"/>
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293 </outputs>
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294
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295 <tests>
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296 <!-- test w gstacks output as input and default options -->
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297 <test>
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298 <param name="options_usage|input_type" value="stacks" />
4
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299 <param name="options_usage|input_aln">
0
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300 <collection type="list">
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301 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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302 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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303 </collection>
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304 </param>
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305 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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306 <param name="add_log" value="yes" />
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307 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
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308 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
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309 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
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310 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
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311 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
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312 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
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313 <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
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314 </test>
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315 <!-- test w gstacks output as input, wo popmap, and default options -->
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316 <test>
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317 <param name="options_usage|input_type" value="stacks" />
4
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318 <param name="options_usage|input_aln">
0
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319 <collection type="list">
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320 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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321 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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322 </collection>
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323 </param>
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324 <param name="add_log" value="yes" />
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325 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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326 </test>
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327 <!-- test w gstacks output as input and + all outputs -->
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328 <test>
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329 <param name="options_usage|input_type" value="stacks" />
4
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330 <param name="options_usage|input_aln">
0
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331 <collection type="list">
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332 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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333 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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334 </collection>
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335 </param>
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336 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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337 <param name="add_log" value="yes" />
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338 <param name="advanced_options|log_fst_comp" value="yes"/>
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339 <param name="fstats_conditional|fstats" value="yes"/>
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340 <param name="populations_output|fasta_loci" value="yes"/>
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341 <param name="populations_output|fasta_samples" value="yes"/>
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342 <param name="populations_output|fasta_samples_raw" value="yes"/>
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343 <param name="populations_output|phylip" value="yes"/>
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344 <param name="populations_output|phylip_var" value="yes"/>
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345 <param name="populations_output|genepop" value="yes"/>
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346 <param name="populations_output|vcf" value="yes"/>
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347 <param name="populations_output|plink" value="yes"/>
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348 <param name="populations_output|structure" value="yes"/>
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349 <param name="populations_output|radpainter" value="yes"/>
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350 <assert_command>
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351 <has_text text="--log_fst_comp" />
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352 </assert_command>
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353 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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354 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
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355 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
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356 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/>
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357 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
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358 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
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359 <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
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360
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361 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
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362 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
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363 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
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364 <output ftype="tabular" name="out_fasta_strict" value="populations/populations.loci.fa" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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365 <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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366 <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" lines_diff="2"/>
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367 <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/>
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368 <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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369 <output ftype="tabular" name="out_phylip_all_pop_var" value="populations/populations.var.phylip" lines_diff="2"/>
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370 <output ftype="tabular" name="out_phylip_all_loci_var" value="populations/populations.var.phylip.log" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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371 <output ftype="tabular" name="out_genepop_snps" value="populations/populations.snps.genepop" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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372 <output ftype="tabular" name="out_genepop_haps" value="populations/populations.haps.genepop" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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373 <output ftype="vcf" name="out_vcf_haplotypes_snps" value="populations/populations.snps.vcf" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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374 <output ftype="vcf" name="out_vcf_haplotypes_haps" value="populations/populations.haps.vcf" lines_diff="2"/>
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375 <output ftype="tabular" name="out_plink_markers" value="populations/populations.plink.map" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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376 <output ftype="tabular" name="out_plink_genotypes" value="populations/populations.plink.ped" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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377 <output ftype="tabular" name="out_structure" value="populations/populations.structure" lines_diff="2"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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378 <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter"/>
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379 </test>
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380 <!-- test w vcf input and default options, just checking if finished -->
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381 <test>
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382 <param name="options_usage|input_type" value="vcf" />
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383 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.tsv"/>
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384 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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385 <param name="add_log" value="yes" />
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386 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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387 </test>
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388 <!-- test w gstacks output as input and non default filtering -->
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389 <test>
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390 <param name="options_usage|input_type" value="stacks" />
4
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391 <param name="options_usage|input_aln">
0
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392 <collection type="list">
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393 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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394 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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395 </collection>
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396 </param>
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397 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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398 <param name="add_log" value="yes" />
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399 <section name="options_filtering">
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400 <param name="minperc" value="0.1"/>
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401 <param name="minpop" value="2"/>
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402 <param name="minminor" value="0.01" />
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403 <param name="min_mac" value="1"/>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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404 <param name="max_obs_het" value="0.8" />
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405 <param name="filter_single_snp" value="--write_random_snp"/>
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406 <param name="blacklist" value="blacklist.tsv" ftype="tabular" />
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407 </section>
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408 <assert_command>
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409 <has_text text="-r 0.1" />
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410 <has_text text="-p 2" />
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411 <has_text text="--min_maf 0.01" />
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412 <has_text text="--min_mac 1" />
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413 <has_text text="--max_obs_het 0.8" />
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414 <has_text text="--write_random_snp" />
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415 <has_text text="-B " />
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416 </assert_command>
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417 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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418 </test>
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419 <!-- test w gstacks output as input and non default merging/hwe -->
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420 <test>
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421 <param name="options_usage|input_type" value="stacks" />
4
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422 <param name="options_usage|input_aln">
0
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423 <collection type="list">
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424 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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425 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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426 </collection>
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427 </param>
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428 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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429 <section name="merge_phase">
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430 <param name="enzyme" value="ecoRI"/>
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431 <param name="merge_sites" value="yes"/>
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432 <param name="merge_prune_lim" value="0.9" />
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433 </section>
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434 <section name="locus_stats">
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435 <param name="hwe" value="yes" />
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436 </section>
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437 <param name="add_log" value="yes" />
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438 <assert_command>
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439 <has_text text="-e ecoRI" />
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440 <has_text text="--merge_sites" />
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441 <has_text text="--merge_prune_lim 0.9" />
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442 <has_text text="--hwe" />
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443 </assert_command>
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444 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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445 </test>
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446 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
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447 <test>
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448 <param name="options_usage|input_type" value="stacks" />
4
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449 <param name="options_usage|input_aln">
0
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450 <collection type="list">
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451 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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452 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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453 </collection>
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454 </param>
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455 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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456 <conditional name="fstats_conditional">
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457 <param name="fstats" value="yes" />
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458 <conditional name="correction_select">
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459 <param name="correction" value="bonferroni_gen"/>
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460 <param name="pcutoff" value="0.01" />
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461 </conditional>
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462 </conditional>
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463 <conditional name="options_kernel">
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464 <param name="kernel" value="-k" />
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465 <param name="sigma" value="150001" />
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466 </conditional>
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467 <conditional name="bootstrap_resampling_mode">
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468 <param name="bootstrap_all" value="--bootstrap" />
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469 </conditional>
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470 <param name="bootstrap_reps" value="23" />
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471 <param name="add_log" value="yes" />
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472 <assert_command>
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473 <has_text text="--fstats" />
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474 <has_text text="--fst_correction bonferroni_gen" />
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475 <has_text text="--p_value_cutoff 0.01" />
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476 <has_text text="-k " />
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477 <has_text text="--sigma 150001" />
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478 <has_text text="--bootstrap" />
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479 <has_text text="--bootstrap_reps 23" />
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480 </assert_command>
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481 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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482 </test>
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483
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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484
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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485
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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486 <!-- TODO test wo popmap -->
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487
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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488 <!-- <test>
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489 <param name="options_usage|input_type" value="stacks" />
4
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diff changeset
490 <param name="options_usage|input_aln">
0
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491 <collection type="list">
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492 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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493 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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494 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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495 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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496 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
497 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
498 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
499 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
500 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
501 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
502 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
503 </collection>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
504 </param>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
505 <param name="popmap" ftype="tabular" value="denovo_map/popmap.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
506 <param name="fstats_conditional|fstat" value="yes" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
507 <param name="fstats_conditional|correction_select|correction" value="p_value" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
508
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
509 <param name="populations_output|ordered_export" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
510 <param name="populations_output|vcf" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
511 <param name="populations_output|vcf_haplotypes" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
512 <param name="populations_output|genepop" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
513 <param name="populations_output|structure" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
514 <param name="populations_output|fasta_loci" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
515 <param name="populations_output|fasta_samples" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
516 <param name="populations_output|hzar" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
517 <param name="populations_output|phase" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
518 <param name="populations_output|fastphase" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
519 <param name="populations_output|beagle" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
520 <param name="populations_output|beagle_phased" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
521 <param name="populations_output|plink" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
522 <param name="populations_output|phylip" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
523 <param name="populations_output|phylip_var" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
524 <param name="populations_output|phylip_var_all" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
525 <param name="populations_output|treemix" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
526
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
527 <param name="merge_phase|enzyme" value="ecoRI" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
528
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
529 <output name="output_summary">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
530 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
531 <has_text text="Stacks Statistics" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
532 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
533 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
534
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
535 <output name="out_haplotypes">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
536 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
537 <has_text text="PopA_01" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
538 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
539 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
540 <output name="out_hapstats">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
541 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
542 <has_text text="Smoothed Gene Diversity" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
543 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
544 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
545 <output name="out_populations_log">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
546 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
547 <has_text text="populations version" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
548 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
549 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
550 <output name="out_sumstats_sum">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
551 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
552 <has_text text="Polymorphic Sites" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
553 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
554 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
555 <output name="out_sumstats">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
556 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
557 <has_text text="Smoothed Pi" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
558 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
559 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
560 <output name="out_vcf">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
561 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
562 <has_text text="fileformat=VCFv4.2" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
563 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
564 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
565 <output name="out_treemix_pop">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
566 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
567 <has_text text="TreeMix v1.1;" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
568 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
569 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
570 <output name="out_fasta">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
571 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
572 <has_text text="AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
573 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
574 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
575 </test>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
576 <test>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
577 <param name="options_usage|input_type" value="vcf" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
578 <param name="options_usage|input_vcf" value="populations/batch_1.vcf" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
579 <param name="popmap" ftype="tabular" value="denovo_map/popmap.tsv" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
580 <param name="options_filtering|correction_select|correction" value="p_value" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
581
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
582 <param name="populations_output|ordered_export" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
583 <param name="populations_output|vcf" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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584 <param name="populations_output|vcf_haplotypes" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
585 <param name="populations_output|genepop" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
586 <param name="populations_output|structure" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
587 <param name="populations_output|fasta_loci" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
588 <param name="populations_output|fasta_samples" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
589 <param name="populations_output|hzar" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
590 <param name="populations_output|phase" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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591 <param name="populations_output|fastphase" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
592 <param name="populations_output|beagle" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
593 <param name="populations_output|beagle_phased" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
594 <param name="populations_output|plink" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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595 <param name="populations_output|phylip" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
596 <param name="populations_output|phylip_var" value="true" />
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diff changeset
597 <param name="populations_output|phylip_var_all" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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598 <param name="populations_output|treemix" value="true" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
599
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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600 <param name="populations_output|options_genomic|genomic" value="false" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
601
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
602 <output name="output_summary">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
603 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
604 <has_text text="Stacks Statistics" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
605 </assert_contents>
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diff changeset
606 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
607
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
608 <output name="out_haplotypes">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
609 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
610 <has_text text="PopA_01" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
611 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
612 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
613 <output name="out_hapstats">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
614 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
615 <has_text text="Smoothed Gene Diversity" />
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616 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
617 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
618 <output name="out_populations_log">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
619 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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620 <has_text text="populations version" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
621 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
622 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
623 <output name="out_sumstats_sum">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
624 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
625 <has_text text="Polymorphic Sites" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
626 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
627 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
628 <output name="out_sumstats">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
629 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
630 <has_text text="Smoothed Pi" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
631 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
632 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
633 <output name="out_vcf">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
634 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
635 <has_text text="fileformat=VCFv4.2" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
636 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
637 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
638 <output name="out_treemix_pop">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
639 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
640 <has_text text="TreeMix v1.1;" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
641 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
642 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
643 <output name="out_fasta">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
644 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
645 <has_text text="CLocus_0_Sample_1_Locus_0_Allele_1" />
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
646 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
647 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
648 </test>-->
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
649 </tests>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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diff changeset
650 <help>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
651 <![CDATA[
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
652 .. class:: infomark
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diff changeset
653
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
654 **What it does**
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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655
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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656 This program will be executed in place of the genotypes program when a population is being processed through the pipeline. A map specifiying which individuals belong to which population is submitted to the program and the program will then calculate population genetics statistics, expected/observed heterzygosity, π, and FIS at each nucleotide position. The populations program will compare all populations pairwise to compute FST. If a set of data is reference aligned, then a kernel-smoothed FST will also be calculated.
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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657
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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658 --------
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
659
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
660 **Input files**
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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661
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
662 Output from denovo_map or ref_map
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
663
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
664 - Population map::
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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665
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
666 indv_01 1
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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667 indv_02 1
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
668 indv_03 1
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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669 indv_04 2
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
670 indv_05 2
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
671 indv_06 2
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
672
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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673
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674 **Output files**
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675
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676 - XXX.tags.tsv file
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677
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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678 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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679
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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680 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.
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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681
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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682
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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683 - XXX.snps.tsv file
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684
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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685 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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686
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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687 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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688
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689
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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690 - XXX.alleles.tsv file
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691
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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692 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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693
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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694
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695 - XXX.matches.tsv file
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696
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697 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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698
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699 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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700
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701
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702 - other files:
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703
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704 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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705
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706 @STACKS_INFOS@
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707 ]]>
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708 </help>
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709 <expand macro="citation" />
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710 </tool>