Mercurial > repos > matthias > stacks2_populations

annotate stacks_populations.xml @ 2:9dbc08d545db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
author matthias
date Fri, 30 Nov 2018 07:41:15 -0500
parents 3950b915b7cf
children d530aff416bd
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2
9dbc08d545db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
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1 <tool id="stacks2_populations" name="Stacks2: populations" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
0
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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_col
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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">
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154 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
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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>
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178 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing Whitelisted 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 Blacklisted markers to be excluded from the export" />
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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 <!-- TODO are two levels of conditionals really necessary -->
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198 <conditional name="fstats_conditional">
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199 <param name="fstats" argument="--fstats" type="select" label="Enable SNP and haplotype-based F statistics" >
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200 <option value="no">No</option>
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201 <option value="yes">Yes</option>
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202 </param>
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203 <when value="no"/>
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204 <when value="yes">
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205 <conditional name="correction_select">
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206 <param name="correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values" >
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207 <option value="no_corr">No correction</option>
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208 <option value="p_value">p_value</option>
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209 <option value="bonferroni_win">bonferroni_win</option>
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210 <option value="bonferroni_gen">bonferroni_gen</option>
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211 </param>
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212 <when value="no_corr"/>
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213 <when value="p_value">
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214 <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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215 </when>
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216 <when value="bonferroni_win">
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217 <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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218 </when>
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219 <when value="bonferroni_gen">
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220 <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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221 </when>
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222 </conditional>
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223 </when>
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224 </conditional>
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225
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226 <!-- File output options -->
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227 <section name="populations_output" title="Output options" expanded="true">
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228 <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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229 <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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230 <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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231 <param name="vcf" argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" />
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232 <param name="genepop" argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" />
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233 <param name="structure" argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" />
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234 <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="output results in fineRADstructure/RADpainter format" />
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235 <!--<param name="phase" argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" />-->
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236 <param name="fastphase" argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" />
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237 <param name="plink" argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" />
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238 <!--<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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239 <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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240 <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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241 <!--<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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242 <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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243 <param argument="--no_hap_exports" truevalue="--no_hap_exports" falsevalue="" type="boolean" checked="false" label="omit haplotype outputs" />
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244 <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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245 </section>
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246
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247 <!-- Kernel-smoothing algorithm -->
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248 <section name="kernel_smoothing" title="Kernel smoothing" expanded="false">
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249 <conditional name="options_kernel">
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250 <param name="kernel" type="select" label="enable kernel-smoothed calculations" >
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251 <option value="">No</option>
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252 <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st</option>
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253 <option value="--smooth_fstats">For Fst, Fst', and Phi_st</option>
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254 <option value="--smooth_popstats">For Pi and Fis</option>
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255 </param>
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256 <when value=""/>
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257 <when value="-k">
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258 <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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259 </when>
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260 <when value="--smooth_fstats">
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261 <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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262 </when>
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263 <when value="--smooth_popstats">
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264 <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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265 </when>
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266 </conditional>
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267 <conditional name="bootstrap_resampling_mode">
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268 <param name="bootstrap_all" argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics" >
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269 <option value="">No</option>
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270 <option value="--bootstrap">Yes</option>
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271 </param>
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272 <when value="--bootstrap">
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273 </when>
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274 <when value="">
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275 <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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276 <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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277 <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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278 <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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279 </when>
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280 </conditional>
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281 <param name="bootstrap_reps" argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" />
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282 <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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283 </section>
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284
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285 <!-- Output options -->
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286 <section name="advanced_options" title="Advanced options" expanded="False">
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287 <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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288 </section>
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289 <expand macro="in_log"/>
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290 </inputs>
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291 <outputs>
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292 <expand macro="out_log"/>
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293 <expand macro="populations_output_full"/>
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294 </outputs>
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295
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296 <tests>
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297 <!-- test w gstacks output as input and default options -->
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298 <test>
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299 <param name="options_usage|input_type" value="stacks" />
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300 <param name="options_usage|input_col">
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301 <collection type="list">
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302 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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303 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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304 </collection>
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305 </param>
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306 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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307 <param name="add_log" value="yes" />
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308 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
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309 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
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310 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
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311 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
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312 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
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313 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
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314 <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
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315 </test>
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316 <!-- test w gstacks output as input, wo popmap, and default options -->
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317 <test>
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318 <param name="options_usage|input_type" value="stacks" />
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319 <param name="options_usage|input_col">
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320 <collection type="list">
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321 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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322 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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323 </collection>
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324 </param>
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325 <param name="add_log" value="yes" />
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326 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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327 </test>
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328 <!-- test w gstacks output as input and + all outputs -->
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329 <test>
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330 <param name="options_usage|input_type" value="stacks" />
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331 <param name="options_usage|input_col">
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332 <collection type="list">
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333 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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334 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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335 </collection>
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336 </param>
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337 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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338 <param name="add_log" value="yes" />
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339 <param name="advanced_options|log_fst_comp" value="yes"/>
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340 <param name="fstats_conditional|fstats" value="yes"/>
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341 <param name="populations_output|fasta_loci" value="yes"/>
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342 <param name="populations_output|fasta_samples" value="yes"/>
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343 <param name="populations_output|fasta_samples_raw" value="yes"/>
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344 <param name="populations_output|phylip" value="yes"/>
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345 <param name="populations_output|phylip_var" value="yes"/>
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346 <param name="populations_output|genepop" value="yes"/>
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347 <param name="populations_output|vcf" value="yes"/>
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348 <param name="populations_output|plink" value="yes"/>
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349 <param name="populations_output|structure" value="yes"/>
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350 <param name="populations_output|radpainter" value="yes"/>
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351 <assert_command>
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352 <has_text text="--log_fst_comp" />
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353 </assert_command>
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354 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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355 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
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356 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
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357 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/>
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358 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
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359 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
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360 <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
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361
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362 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
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363 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
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364 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
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365 <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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366 <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" lines_diff="2"/>
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367 <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" lines_diff="2"/>
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368 <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/>
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369 <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/>
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370 <output ftype="tabular" name="out_phylip_all_pop_var" value="populations/populations.var.phylip" lines_diff="2"/>
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371 <output ftype="tabular" name="out_phylip_all_loci_var" value="populations/populations.var.phylip.log" lines_diff="2"/>
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372 <output ftype="tabular" name="out_genepop_snps" value="populations/populations.snps.genepop" lines_diff="2"/>
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373 <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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374 <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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diff changeset
375 <output ftype="vcf" name="out_vcf_haplotypes_haps" value="populations/populations.haps.vcf" lines_diff="2"/>
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376 <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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377 <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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378 <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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379 <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter"/>
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380 </test>
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381 <!-- test w vcf input and default options, just checking if finished -->
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382 <test>
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383 <param name="options_usage|input_type" value="vcf" />
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384 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.tsv"/>
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385 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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386 <param name="add_log" value="yes" />
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387 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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388 </test>
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389 <!-- test w gstacks output as input and non default filtering -->
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390 <test>
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391 <param name="options_usage|input_type" value="stacks" />
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392 <param name="options_usage|input_col">
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393 <collection type="list">
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394 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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395 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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396 </collection>
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397 </param>
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398 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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399 <param name="add_log" value="yes" />
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400 <section name="options_filtering">
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401 <param name="minperc" value="0.1"/>
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402 <param name="minpop" value="2"/>
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403 <param name="minminor" value="0.01" />
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404 <param name="min_mac" value="1"/>
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405 <param name="max_obs_het" value="0.8" />
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406 <param name="filter_single_snp" value="--write_random_snp"/>
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407 <param name="blacklist" value="blacklist.tsv" ftype="tabular" />
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408 </section>
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409 <assert_command>
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410 <has_text text="-r 0.1" />
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411 <has_text text="-p 2" />
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412 <has_text text="--min_maf 0.01" />
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413 <has_text text="--min_mac 1" />
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414 <has_text text="--max_obs_het 0.8" />
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415 <has_text text="--write_random_snp" />
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416 <has_text text="-B " />
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417 </assert_command>
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418 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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419 </test>
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420 <!-- test w gstacks output as input and non default merging/hwe -->
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421 <test>
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422 <param name="options_usage|input_type" value="stacks" />
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423 <param name="options_usage|input_col">
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424 <collection type="list">
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425 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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426 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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427 </collection>
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428 </param>
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429 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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430 <section name="merge_phase">
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431 <param name="enzyme" value="ecoRI"/>
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432 <param name="merge_sites" value="yes"/>
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433 <param name="merge_prune_lim" value="0.9" />
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434 </section>
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435 <section name="locus_stats">
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436 <param name="hwe" value="yes" />
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437 </section>
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438 <param name="add_log" value="yes" />
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439 <assert_command>
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440 <has_text text="-e ecoRI" />
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441 <has_text text="--merge_sites" />
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442 <has_text text="--merge_prune_lim 0.9" />
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443 <has_text text="--hwe" />
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444 </assert_command>
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445 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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446 </test>
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447 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
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448 <test>
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449 <param name="options_usage|input_type" value="stacks" />
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450 <param name="options_usage|input_col">
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451 <collection type="list">
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452 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.tsv" />
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453 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" />
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454 </collection>
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455 </param>
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456 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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457 <conditional name="fstats_conditional">
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458 <param name="fstats" value="yes" />
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459 <conditional name="correction_select">
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460 <param name="correction" value="bonferroni_gen"/>
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461 <param name="pcutoff" value="0.01" />
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462 </conditional>
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463 </conditional>
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464 <conditional name="options_kernel">
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465 <param name="kernel" value="-k" />
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466 <param name="sigma" value="150001" />
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467 </conditional>
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468 <conditional name="bootstrap_resampling_mode">
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469 <param name="bootstrap_all" value="--bootstrap" />
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470 </conditional>
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471 <param name="bootstrap_reps" value="23" />
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472 <param name="add_log" value="yes" />
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473 <assert_command>
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474 <has_text text="--fstats" />
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475 <has_text text="--fst_correction bonferroni_gen" />
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476 <has_text text="--p_value_cutoff 0.01" />
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477 <has_text text="-k " />
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478 <has_text text="--sigma 150001" />
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479 <has_text text="--bootstrap" />
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480 <has_text text="--bootstrap_reps 23" />
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481 </assert_command>
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482 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output>
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483 </test>
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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
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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487 <!-- TODO test wo popmap -->
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488
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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489 <!-- <test>
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490 <param name="options_usage|input_type" value="stacks" />
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491 <param name="options_usage|input_col">
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492 <collection type="list">
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493 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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494 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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495 <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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496 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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diff changeset
497 <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
matthias
parents:
diff changeset
498 <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
499 <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
500 <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
501 <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
502 <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
503 <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
504 </collection>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
505 </param>
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="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
507 <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
508 <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
509
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|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
511 <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
512 <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
513 <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
514 <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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <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
522 <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
523 <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
524 <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
525 <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
526 <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
527
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
528 <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
529
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
530 <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
531 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
532 <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
533 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
534 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
535
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
536 <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
537 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
538 <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
539 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
540 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
541 <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
542 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
543 <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
544 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
545 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
546 <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
547 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
548 <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
549 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
550 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
551 <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
552 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
553 <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
554 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
555 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
556 <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
557 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
558 <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
559 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
560 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
561 <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
562 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
563 <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
564 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
565 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
566 <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
567 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
568 <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
569 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
570 </output>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
571 <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
572 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
573 <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
574 </assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
575 </output>
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 <test>
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_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
579 <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
580 <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
581 <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
582
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|ordered_export" 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" 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|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
586 <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
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diff changeset
587 <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
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diff changeset
588 <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
589 <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
590 <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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591 <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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592 <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
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diff changeset
593 <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
594 <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
595 <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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diff changeset
596 <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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597 <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
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diff changeset
598 <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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diff changeset
599 <param name="populations_output|treemix" value="true" />
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diff changeset
600
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 <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
602
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
603 <output name="output_summary">
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 <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
605 <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
606 </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
607 </output>
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diff changeset
608
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
609 <output name="out_haplotypes">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
610 <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
611 <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
612 </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
613 </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
614 <output name="out_hapstats">
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
615 <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
616 <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
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diff changeset
617 </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
618 </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
619 <output name="out_populations_log">
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
620 <assert_contents>
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
621 <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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622 </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
623 </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
624 <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
625 <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
626 <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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627 </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
628 </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
629 <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
630 <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
631 <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
632 </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
633 </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
634 <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
635 <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
636 <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
637 </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
638 </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
639 <output name="out_treemix_pop">
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 <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
641 <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
642 </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
643 </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
644 <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
645 <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
646 <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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647 </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
648 </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
649 </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
650 </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
651 <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
652 <![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
653 .. class:: infomark
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
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
655 **What it does**
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656
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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657 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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658
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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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
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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diff changeset
661 **Input files**
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
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 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
664
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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665 - Population map::
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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666
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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667 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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668 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
669 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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670 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
671 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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672 indv_06 2
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673
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674
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675 **Output files**
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676
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677 - XXX.tags.tsv file
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678
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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679 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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680
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681 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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682
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683
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684 - XXX.snps.tsv file
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685
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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686 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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687
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688 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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689
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690
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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691 - XXX.alleles.tsv file
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692
3950b915b7cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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693 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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694
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695
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696 - XXX.matches.tsv file
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697
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698 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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699
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700 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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701
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702
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703 - other files:
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704
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705 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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706
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707 @STACKS_INFOS@
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708 ]]>
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709 </help>
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710 <expand macro="citation" />
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711 </tool>