Mercurial > repos > iuc > stacks2_populations

annotate stacks_populations.xml @ 6:e2db212d64ad draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author iuc
date Thu, 14 Apr 2022 09:21:25 +0000
parents 887cf585cafc
children 564c33e5c3e3
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6
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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1 <tool id="stacks2_populations" name="Stacks2: populations" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
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2 <description>Calculate population-level summary statistics</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="version_cmd"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #import re
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10
1
9a44832748c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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11 mkdir stacks_inputs stacks_outputs &&
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12
1
9a44832748c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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13 #if $output_log
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14 ln -s '$output_log' stacks_outputs/populations.log &&
9a44832748c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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15 #end if
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16
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17 #if str($options_usage.input_type) == 'stacks'
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18 #for $input_file in $options_usage.input_aln
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19 #set $filename = str($input_file.element_identifier)
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20 #if $filename == "catalog.calls" or $filename == "catalog.fa.gz":
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 ln -s '${input_file}' 'stacks_inputs/${filename}' &&
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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22 #elif $filename == "catalog.calls.vcf":
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 gzip -c '${input_file}' > stacks_inputs/catalog.calls &&
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24 #end if
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25 #end for
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26 #else if str($options_usage.input_type) == 'vcf'
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27 ln -s '$options_usage.input_vcf' 'stacks_inputs/input.vcf' &&
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28 #end if
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29
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30 populations
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31
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32 -t \${GALAXY_SLOTS:-1}
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33
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34 #if str($options_usage.input_type) == 'vcf'
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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35 -V stacks_inputs/input.vcf
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36 #else
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37 -P stacks_inputs
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38 #end if
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39 -O stacks_outputs
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40
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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41 #if str($popmap) != 'None':
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42 -M '$popmap'
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43 #end if
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44 #if str($batch_size) != '':
2
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45 --batch-size '$batch_size'
0
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46 #end if
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47
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48 ## Data filtering
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49
1
9a44832748c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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50 --min-populations $options_filtering.minpop
9a44832748c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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51 --min-samples-per-pop $options_filtering.minperc
9a44832748c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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52 --min-samples-overall $options_filtering.min_samples_overall
0
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53 $options_filtering.filter_haplotype_wise
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54 --min-maf $options_filtering.min_maf
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55 --min-mac $options_filtering.min_mac
0
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56 #if str($options_filtering.max_obs_het)
3
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57 --max-obs-het $options_filtering.max_obs_het
0
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58 #end if
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59 ## deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
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60 ## #if str($options_filtering.lnl)
3
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61 ## --lnl-lim $options_filtering.lnl
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62 ## #end if
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63 $options_filtering.filter_single_snp
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64 #if $options_filtering.blacklist
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65 -B '$options_filtering.blacklist'
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66 #end if
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67 #if $options_filtering.whitelist
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68 -W '$options_filtering.whitelist'
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69 #end if
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70
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71 ## Merging and Phasing:
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72 #if str($merge_phase.enzyme) != '':
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73 -e $merge_phase.enzyme
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74 #end if
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75 $merge_phase.merge_sites
3
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76 --merge-prune-lim $merge_phase.merge_prune_lim
0
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77
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78 ## Locus stats:
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79 $locus_stats.hwe
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80
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81 ## Fstats
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82 #if str($fstats_conditional.fstats) != 'no':
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83 --fstats
3
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84 $fstats_conditional.fst_correction
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85 #if $fstats_conditional.fst_correction
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86 --p-value-cutoff $fstats_conditional.p_value_cutoff
0
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87 #end if
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88 #end if
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89
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90 ## Kernel-smoothing algorithm:
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91 $kernel_smoothing.options_kernel.kernel
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92 #if str($kernel_smoothing.options_kernel.kernel)!='':
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93 --sigma $kernel_smoothing.options_kernel.sigma
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94 #end if
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95 #if $kernel_smoothing.bootstrap_resampling_mode.bootstrap
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96 --bootstrap
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97 #else
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98 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_pifis
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99 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_fst
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100 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_div
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101 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist
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102 #end if
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103
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104 #if $kernel_smoothing.bootstrap_resampling_mode.bootstrap 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 $kernel_smoothing.bootstrap_resampling_mode.bootstrap_phist:
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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105 #if str($kernel_smoothing.bootstrap_reps)
3
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106 --bootstrap-reps $kernel_smoothing.bootstrap_reps
0
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107 #end if
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108 #if $kernel_smoothing.bootstrap_wl
3
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109 --bootstrap-wl '$kernel_smoothing.bootstrap_wl'
0
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110 #end if
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111 #end if
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112
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113 ## File output options:
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114
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115 $populations_output.ordered_export
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116 $populations_output.fasta_loci
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117 $populations_output.fasta_samples
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118 $populations_output.vcf
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119 $populations_output.genepop
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120 $populations_output.structure
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121 $populations_output.radpainter
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122 $populations_output.plink
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123 $populations_output.hzar
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124 $populations_output.phylip
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125 $populations_output.phylip_var
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126 ##$populations_output.phylip_var_all
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127 $populations_output.treemix
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128 $populations_output.no_hap_exports
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129 $populations_output.fasta_samples_raw
4
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130 $populations_output.gtf
0
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131
3
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132 #if $genetic_map_options.map_type:
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133 --map-type $genetic_map_options.map_type
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134 #end if
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135 #if $genetic_map_options.map_format
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136 --map-format $genetic_map_options.map_format
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137 #end if
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138
0
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139 ## Additional options:
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140
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141 $advanced_options.log_fst_comp
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142
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143 ## populations outputs log info to stdout for vcf input
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144 ## for gstacks input it creates stacks_output/population.log
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145 ## in the latter case we take the log file
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iuc
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146 ## also for vcf input the output files are named input.p....
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147 ## instead of populations...
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148
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149 #if str($options_usage.input_type) == 'vcf'
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150 #if $output_log
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151 > $output_log
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152 #end if
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153 && 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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154 #end if
3
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155
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156 ## move the genotype output (note that in 2.52 there is an inconsistent
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157 ## naming for onemap output and also extensions are inconsistent -> therefore wildcard)
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158 #if $genetic_map_options.map_type and $genetic_map_options.map_format
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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159 && mv stacks_outputs/populations.${genetic_map_options.map_type}.* stacks_outputs/populations.sql.tsv
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160 #end if
0
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161 ]]></command>
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162
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163 <inputs>
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164 <conditional name="options_usage">
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165 <param name="input_type" type="select" label="Input type" help="select input file type" >
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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166 <option value="stacks">Stacks output</option>
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167 <option value="vcf">VCF file</option>
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168 </param>
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169 <when value="stacks">
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170 <expand macro="input_aln_macro"/>
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171 </when>
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172 <when value="vcf">
3
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173 <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V"/>
0
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174 </when>
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175 </conditional>
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176 <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"/>
3
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177 <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)"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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178
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179 <!-- Data Filtering -->
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180 <section name="options_filtering" title="Data filtering options" expanded="true">
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181
3
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182 <param name="minperc" argument="--min-samples-per-pop" 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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183 <param name="minpop" argument="--min-populations" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus"/>
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184 <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus"/>
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185 <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data."/>
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186 <param 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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187 <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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188 <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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189 <!-- deprecated https://groups.google.com/forum/#!msg/stacks-users/jdC7gw_MuK4/1v0FG3u7AwAJ
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190 <param type="float" value="" optional="true" argument="\-\-lnl_lim" label="Filter loci with log likelihood values below this threshold"/>-->
0
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191 <param name="filter_single_snp" type="select" label="Analyse all SNPs per locus" >
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192 <option value="">yes</option>
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193 <option value="--write-single-snp">No: Analyse only the first SNP (--write-single-snp)</option>
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194 <option value="--write-random-snp">No: Analyse only one random SNP (--write-random-snp)</option>
0
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195 </param>
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196 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to include in the export"/>
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197 <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing markers to exclude from the export"/>
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198 </section>
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199
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200 <!-- merging and Phasing -->
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201 <section name="merge_phase" title="Merging and Phasing" expanded="true">
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202 <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" >
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203 <expand macro="enzymes"/>
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204 </param>
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205 <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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206 <param argument="--merge-prune-lim" type="float" value="1.0" min="0.0" max="1.0" label="Fraction of samples possessing both loci to prune remaining samples from analysis" help="for merging adjacent loci"/>
0
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207 </section>
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208
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209 <!-- Locus stats -->
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210 <section name="locus_stats" title="Locus Stats" expanded="true">
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211 <param argument="--hwe" truevalue="--hwe" falsevalue="" type="boolean" checked="false" label="Calculate divergence from Hardy-Weinberg equilibrium for each locus"/>
0
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212 </section>
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213
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214 <!-- Fstats -->
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215 <conditional name="fstats_conditional">
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216 <param argument="--fstats" type="select" label="Enable SNP and haplotype-based F statistics" >
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217 <option value="no">No</option>
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218 <option value="yes">Yes</option>
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219 </param>
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220 <when value="no"/>
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221 <when value="yes">
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222 <param argument="--fst-correction" truevalue="--fst-correction" falsevalue="" type="boolean" checked="false" label="apply a p-value correction to Fst values based on a Fisher's exact test" help=""/>
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223 <param argument="--p-value-cutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default)."/>
0
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224 </when>
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225 </conditional>
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226
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227 <!-- File output options -->
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228 <section name="populations_output" title="Output options" expanded="true">
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229 <param 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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230 <param argument="--fasta-loci" truevalue="--fasta-loci" falsevalue="" type="boolean" checked="false" label="Output locus consensus sequences in FASTA format"/>
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231 <param 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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232 <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/>
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233 <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/>
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234 <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/>
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235 <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/>
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236 <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/>
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237 <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/>
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238 <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/>
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239 <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/>
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240 <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip-var-all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation."/>-->
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241 <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)."/>
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242 <param argument="--no-hap-exports" truevalue="--no-hap-exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs"/>
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243 <param argument="--fasta-samples-raw" truevalue="--fasta-samples-raw" falsevalue="" type="boolean" checked="false" label="Output all haplotypes observed in each sample, for each locus, in FASTA format"/>
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244 <param argument="--gtf" truevalue="--gtf" falsevalue="" type="boolean" checked="false" label="output locus positions in a GTF annotation file"/>
0
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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" help="The options -k and --smooth-fstats implicitly enable --fstats. Note that, in order to set non-default values for --fst-correction or --p-value-cutoff the option --fstats still needs to be enabled in the tool form." >
0
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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 (-k/--smooth)</option>
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253 <option value="--smooth-fstats">For Fst, Fst', and Phi_st (--smooth-fstats)</option>
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254 <option value="--smooth-popstats">For Pi and Fis (--smooth-popstats)</option>
0
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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)"/>
0
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259 </when>
3
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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)"/>
0
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262 </when>
3
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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)"/>
0
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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 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="">
3
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275 <param 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 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 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 argument="--bootstrap-phist" type="boolean" checked="false" truevalue="--bootstrap-phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes."/>
0
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279 </when>
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280 </conditional>
3
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281 <param argument="--bootstrap-reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate"/>
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282 <param argument="--bootstrap-wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist"/>
0
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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">
3
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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 dataset"/>
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288 </section>
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289
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290 <!-- Genetic map output options (population map must specify a genetic cross): -->
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291 <section name="genetic_map_options" title="Genetic map output options (population map must specify a genetic cross)" help="works only if a population map specifying only two groupings: 'parent' and 'progeny'" expanded="false">
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292 <param argument="--map-type" type="select" optional="true" label="genetic map type to write" help="needs to be selected to trigger the additional Genotyping markers output">
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293 <option value="CP">CP</option>
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294 <option value="DH">DH</option>
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295 <option value="F2">F2</option>
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296 <option value="BC1">BC1</option>
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297 </param>
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298 <param argument="--map-format" type="select" optional="true" label="mapping program format to write" help="needs to be selected to trigger the additional Genotyping markers output">
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299 <option value="joinmap">joinmap</option>
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300 <option value="onemap">onemap</option>
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301 <option value="rqtl">rqtl</option>
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302 </param>
0
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303 </section>
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304 <expand macro="in_log"/>
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305 </inputs>
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306 <outputs>
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307 <expand macro="out_log"/>
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308 <expand macro="populations_output_full"/>
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309 </outputs>
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310 <tests>
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311 <!-- test w gstacks output as input and default options -->
3
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312 <test expect_num_outputs="6">
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313 <param name="options_usage|input_type" value="stacks"/>
0
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314 <param name="options_usage|input_aln">
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315 <collection type="list">
3
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316 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
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317 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
0
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318 </collection>
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319 </param>
3
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320 <param name="batch_size" value="9999"/>
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321 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
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322 <param name="batch_size" value="9999"/>
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323 <param name="add_log" value="yes"/>
0
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324 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
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325 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
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326 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
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327 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
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328 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
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329 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
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330 </test>
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331 <!-- test w gstacks output as input, wo popmap, and default options -->
3
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332 <test expect_num_outputs="6">
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333 <param name="options_usage|input_type" value="stacks"/>
0
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334 <param name="options_usage|input_aln">
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335 <collection type="list">
3
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336 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
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337 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
0
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338 </collection>
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339 </param>
3
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340 <param name="add_log" value="yes"/>
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341 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
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342 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
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343 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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344 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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345 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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346 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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347 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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348 <!-- test w gstacks output as input and + all outputs -->
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diff changeset
349 <test expect_num_outputs="27">
3
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iuc
parents: 2
diff changeset
350 <param name="options_usage|input_type" value="stacks"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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351 <param name="options_usage|input_aln">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
352 <collection type="list">
3
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iuc
parents: 2
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353 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
354 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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355 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
356 </param>
3
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iuc
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diff changeset
357 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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358 <param name="add_log" value="yes"/>
6
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iuc
parents: 4
diff changeset
359 <param name="advanced_options|log_fst_comp" value="true"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
360 <param name="fstats_conditional|fstats" value="yes"/>
6
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
361 <param name="populations_output|fasta_loci" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
362 <param name="populations_output|fasta_samples" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
363 <param name="populations_output|fasta_samples_raw" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
364 <param name="populations_output|phylip" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
365 <param name="populations_output|phylip_var" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
366 <param name="populations_output|genepop" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
367 <param name="populations_output|vcf" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
368 <param name="populations_output|hzar" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
369 <param name="populations_output|plink" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
370 <param name="populations_output|structure" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
371 <param name="populations_output|radpainter" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
372 <param name="populations_output|treemix" value="true"/>
e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 4
diff changeset
373 <param name="populations_output|gtf" value="true"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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374 <assert_command>
3
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iuc
parents: 2
diff changeset
375 <has_text text="--log-fst-comp"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
376 </assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
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377 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
378 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
379 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
380 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
381 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
382 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
383
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
384 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
385 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
386 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
387 <output ftype="tabular" name="out_fasta_strict" value="populations/populations.loci.fa" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header -->
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
388 <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " -->
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
389 <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
390 <output ftype="tabular" name="out_phylip_all_pop_fix" value="populations/populations.fixed.phylip" lines_diff="2"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
391 <output ftype="tabular" name="out_phylip_all_loci_fix" value="populations/populations.fixed.phylip.log" lines_diff="2"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
392 <output ftype="tabular" name="out_phylip_all_pop_var" value="populations/populations.var.phylip" compare="sim_size" delta="50"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
393 <output ftype="tabular" name="out_phylip_all_loci_var" value="populations/populations.var.phylip.log" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
394 <output ftype="tabular" name="out_genepop_snps" value="populations/populations.snps.genepop" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
395 <output ftype="tabular" name="out_genepop_haps" value="populations/populations.haps.genepop" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
396 <output ftype="vcf" name="out_vcf_haplotypes_snps" value="populations/populations.snps.vcf" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
397 <output ftype="vcf" name="out_vcf_haplotypes_haps" value="populations/populations.haps.vcf" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
398 <output ftype="tabular" name="out_plink_markers" value="populations/populations.plink.map" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
399 <output ftype="tabular" name="out_plink_genotypes" value="populations/populations.plink.ped" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
400 <output ftype="tabular" name="out_hzar" value="populations/populations.hzar.csv" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
401 <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
402 <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " -->
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
403 <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " -->
4
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
404 <output ftype="gtf" name="out_gtf" value="populations/populations.gtf" lines_diff="2"/><!-- " -->
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
405 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
406 <!-- test w vcf input and default options, just checking if finished -->
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
407 <test expect_num_outputs="6">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
408 <param name="options_usage|input_type" value="vcf"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
409 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
410 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
411 <param name="add_log" value="yes"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
412 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
413 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
414 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
415 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
416 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
417 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
418 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
419 <!-- test w gstacks output as input and non default filtering -->
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
420 <test expect_num_outputs="6">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
421 <param name="options_usage|input_type" value="stacks"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
422 <param name="options_usage|input_aln">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
423 <collection type="list">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
424 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
425 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
426 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
427 </param>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
428 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
429 <param name="add_log" value="yes"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
430 <section name="options_filtering">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
431 <param name="minperc" value="0.1"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
432 <param name="minpop" value="2"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
433 <param name="min_samples_overall" value="0.01"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
434 <param name="filter_haplotype_wise" value="--filter-haplotype-wise"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
435 <param name="min_maf" value="0.01"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
436 <param name="min_mac" value="1"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
437 <param name="max_obs_het" value="0.8"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
438 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
439 </section>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
440 <assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
441 <has_text text="--min-samples-per-pop 0.1"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
442 <has_text text="--min-populations 2"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
443 <has_text text="--min-samples-overall 0.01"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
444 <has_text text="--filter-haplotype-wise"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
445 <has_text text="--min-maf 0.01"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
446 <has_text text="--min-mac 1"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
447 <has_text text="--max-obs-het 0.8"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
448 <has_text text="-B "/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
449 </assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
450 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
451 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
452 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
453 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
454 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
455 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
456 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
457 <!-- test w gstacks output as input and non default filtering (needed because filter-haplotype-wise is incompatible with write_random_snp/write_single_snp) -->
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
458 <test expect_num_outputs="6">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
459 <param name="options_usage|input_type" value="stacks"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
460 <param name="options_usage|input_aln">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
461 <collection type="list">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
462 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
463 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
464 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
465 </param>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
466 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
467 <param name="add_log" value="yes"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
468 <section name="options_filtering">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
469 <param name="minperc" value="0.1"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
470 <param name="minpop" value="2"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
471 <param name="min_samples_overall" value="0.01"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
472 <param name="min_maf" value="0.01"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
473 <param name="min_mac" value="1"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
474 <param name="max_obs_het" value="0.8"/>
1
9a44832748c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
475 <!-- since write_random_snp runs in infinite loop switch to write_single -->
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
476 <param name="filter_single_snp" value="--write-single-snp"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
477 <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
478 </section>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
479 <assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
480 <has_text text="--min-samples-per-pop 0.1"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
481 <has_text text="--min-populations 2"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
482 <has_text text="--min-samples-overall 0.01"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
483 <has_text text="--min-maf 0.01"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
484 <has_text text="--min-mac 1"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
485 <has_text text="--max-obs-het 0.8"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
486 <not_has_text text="--write-random-snp"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
487 <has_text text="-B "/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
488 </assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
489 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
490 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
491 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
492 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
493 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
494 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
495 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
496 <!-- test w gstacks output as input and non default merging/hwe -->
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
497 <test expect_num_outputs="6">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
498 <param name="options_usage|input_type" value="stacks"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
499 <param name="options_usage|input_aln">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
500 <collection type="list">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
501 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
502 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
503 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
504 </param>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
505 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
506 <section name="merge_phase">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
507 <param name="enzyme" value="ecoRI"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
508 <param name="merge_sites" value="yes"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
509 <param name="merge_prune_lim" value="0.9"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
510 </section>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
511 <section name="locus_stats">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
512 <param name="hwe" value="yes"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
513 </section>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
514 <param name="add_log" value="yes"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
515 <assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
516 <has_text text="-e ecoRI"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
517 <has_text text="--merge-sites"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
518 <has_text text="--merge-prune-lim 0.9"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
519 <has_text text="--hwe"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
520 </assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
521 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
522 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
523 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
524 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
525 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
526 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
527 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
528 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
4
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
529 <test expect_num_outputs="9">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
530 <param name="options_usage|input_type" value="stacks"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
531 <param name="options_usage|input_aln">
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
532 <collection type="list">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
533 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
534 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
535 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
536 </param>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
537 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
538 <conditional name="fstats_conditional">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
539 <param name="fstats" value="yes"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
540 <param name="fst_correction" value="--fst-correction"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
541 <param name="p_value_cutoff" value="0.01"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
542 </conditional>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
543 <conditional name="options_kernel">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
544 <param name="kernel" value="-k"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
545 <param name="sigma" value="150001"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
546 </conditional>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
547 <conditional name="bootstrap_resampling_mode">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
548 <param name="bootstrap" value="--bootstrap"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
549 </conditional>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
550 <param name="bootstrap_reps" value="23"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
551 <param name="add_log" value="yes"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
552 <assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
553 <has_text text="--fstats"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
554 <has_text text="--fst-correction"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
555 <has_text text="--p-value-cutoff 0.01"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
556 <has_text text="-k "/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
557 <has_text text="--sigma 150001"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
558 <has_text text="--bootstrap"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
559 <has_text text="--bootstrap-reps 23"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
560 </assert_command>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
561 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
562 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
563 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
564 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
565 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
566 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
4
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
567 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
568 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
569 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
570 </test>
4
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
571 <!-- same as previous test but without fstats parameter in order to check if the filter
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
572 for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
573 is used) -->
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
574 <test expect_num_outputs="9">
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
575 <param name="options_usage|input_type" value="stacks"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
576 <param name="options_usage|input_aln">
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
577 <collection type="list">
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
578 <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
579 <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
580 </collection>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
581 </param>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
582 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
583 <conditional name="fstats_conditional">
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
584 <param name="fstats" value="no"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
585 </conditional>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
586 <conditional name="options_kernel">
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
587 <param name="kernel" value="--smooth-fstats"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
588 <param name="sigma" value="150001"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
589 </conditional>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
590 <conditional name="bootstrap_resampling_mode">
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
591 <param name="bootstrap" value="--bootstrap"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
592 </conditional>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
593 <param name="bootstrap_reps" value="23"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
594 <param name="add_log" value="yes"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
595 <assert_command>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
596 <not_has_text text="--fstats"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
597 <not_has_text text="--fst-correction"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
598 <not_has_text text="--p-value-cutoff 0.01"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
599 <has_text text="--smooth-fstats "/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
600 <has_text text="--sigma 150001"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
601 <has_text text="--bootstrap"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
602 <has_text text="--bootstrap-reps 23"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
603 </assert_command>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
604 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
605 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
606 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
607 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
608 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
609 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
610 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
611 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
612 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
613 </test>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
614 <!-- test w gstacks output as input and default options -->
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
615 <test expect_num_outputs="6">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
616 <param name="options_usage|input_type" value="stacks"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
617 <param name="options_usage|input_aln">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
618 <collection type="list">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
619 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
620 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
621 </collection>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
622 </param>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
623 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
624 <param name="add_log" value="yes"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
625 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
626 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
627 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
628 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
629 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
630 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
631 </test>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
632 <!-- test w gstacks output as input, wo popmap, and Genetic map output options that have been added in 2.5 -->
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
633 <test expect_num_outputs="7">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
634 <param name="options_usage|input_type" value="stacks"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
635 <param name="options_usage|input_aln">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
636 <collection type="list">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
637 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
638 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
639 </collection>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
640 </param>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
641 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks_genotypes.tsv"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
642 <section name="genetic_map_options">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
643 <param name="map_type" value="CP"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
644 <param name="map_format" value="joinmap"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
645 </section>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
646 <param name="add_log" value="yes"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
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647 <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
648 <output ftype="txt" name="out_sql" file="populations/populations.CP.joinmap.loc" lines_diff="4"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
649 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
650 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
651 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
652 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
653 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
654 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
655 </tests>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
656 <help>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
657 <![CDATA[
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
658 .. class:: infomark
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
659
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
660 **What it does**
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
661
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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662 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.
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
663
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
664 --------
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
665
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
666 **Input files**
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
667
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
668 Output from denovo_map or ref_map
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
669
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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670 - Population map::
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
671
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
672 indv_01 1
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
673 indv_02 1
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
674 indv_03 1
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
675 indv_04 2
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
676 indv_05 2
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
677 indv_06 2
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
678
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
679
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
680 **Output files**
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
681
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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682 - XXX.tags.tsv file
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
683
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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684 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
685
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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686 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.
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
687
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
688
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
689 - XXX.snps.tsv file
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
690
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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691 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
692
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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693 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
694
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
695
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
696 - XXX.alleles.tsv file
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
697
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
698 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
699
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
700
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
701 - XXX.matches.tsv file
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
702
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
703 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
704
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
705 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.
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
706
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
707
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
708 - other files:
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
709
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
710 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
711
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
712 @STACKS_INFOS@
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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713 ]]>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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714 </help>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
715 <expand macro="citation"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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716 </tool>