annotate stacks_populations.xml @ 8:564c33e5c3e3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
author iuc
date Mon, 23 May 2022 17:47:23 +0000
parents e2db212d64ad
children
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e2db212d64ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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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"/>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
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11 mkdir stacks_inputs stacks_outputs &&
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12
1
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13 #if $output_log
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14 ln -s '$output_log' stacks_outputs/populations.log &&
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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)
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
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34 #if str($options_usage.input_type) == 'vcf'
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35 -V stacks_inputs/input.vcf
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36 #else
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37 -P stacks_inputs
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38 #end if
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39 -O stacks_outputs
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40
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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41 #if str($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) != '':
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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
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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 $advanced_options.log_fst_comp
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142
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143 ## populations outputs log info to stdout for vcf input
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144 ## for gstacks input it creates stacks_output/population.log
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145 ## in the latter case we take the log file
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146 ## also for vcf input the output files are named input.p....
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147 ## instead of populations...
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148
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149 #if str($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>
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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>
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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>
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346 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
0
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347 </test>
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348 <!-- test w gstacks output as input and + all outputs -->
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349 <test expect_num_outputs="28">
3
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350 <param name="options_usage|input_type" value="stacks"/>
0
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351 <param name="options_usage|input_aln">
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352 <collection type="list">
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353 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
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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
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355 </collection>
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356 </param>
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357 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
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358 <param name="add_log" value="yes"/>
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359 <param name="advanced_options|log_fst_comp" value="true"/>
0
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360 <param name="fstats_conditional|fstats" value="yes"/>
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361 <param name="populations_output|fasta_loci" value="true"/>
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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370 <param name="populations_output|structure" value="true"/>
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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"
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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"
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373 <param name="populations_output|gtf" value="true"/>
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374 <assert_command>
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375 <has_text text="--log-fst-comp"/>
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376 </assert_command>
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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
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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
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379 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
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380 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2">
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
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381 <assert_contents>
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382 <has_text text="Calculating F statistics...done."/>
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383 </assert_contents>
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384 </output>
0
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385 <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
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386 <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
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diff changeset
387
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388 <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
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389 <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
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390 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
8
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
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diff changeset
391 <output_collection name="out_fstats_popcompare" type="list" count="0"/>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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392 <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"
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393 <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
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394 <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
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395 <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
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396 <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
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397 <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
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diff changeset
398 <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
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399 <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
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400 <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
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401 <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
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diff changeset
402 <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
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403 <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
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404 <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
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405 <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
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406 <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
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407 <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
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408 <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " -->
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409 <output ftype="gtf" name="out_gtf" value="populations/populations.gtf" lines_diff="2"/><!-- " -->
0
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410 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
411 <!-- test w vcf input and default options, just checking if finished -->
3
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412 <test expect_num_outputs="6">
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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413 <param name="options_usage|input_type" value="vcf"/>
0
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414 <param name="options_usage|input_vcf" ftype="vcf" value="gstacks/catalog.calls.vcf"/>
3
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415 <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"
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416 <param name="add_log" value="yes"/>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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417 <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
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418 <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"
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419 <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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diff changeset
420 <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
421 <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
422 <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
423 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
424 <!-- 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
425 <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
426 <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
427 <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
428 <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
429 <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
430 <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
431 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
432 </param>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
433 <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
434 <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
435 <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
436 <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
437 <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
438 <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
439 <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
440 <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
441 <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
442 <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
443 <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
444 </section>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
445 <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
446 <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
447 <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
448 <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
449 <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
450 <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
451 <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
452 <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
453 <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
454 </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
455 <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
456 <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
457 <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
458 <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
459 <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
460 <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
461 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
462 <!-- 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
463 <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
464 <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
465 <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
466 <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
467 <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
468 <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
469 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
470 </param>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
471 <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
472 <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
473 <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
474 <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
475 <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
476 <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
477 <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
478 <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
479 <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
480 <!-- 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
481 <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
482 <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
483 </section>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
484 <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
485 <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
486 <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
487 <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
488 <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
489 <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
490 <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
491 <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
492 <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
493 </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
494 <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
495 <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
496 <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
497 <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
498 <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
499 <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
500 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
501 <!-- 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
502 <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
503 <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
504 <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
505 <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
506 <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
507 <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
508 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
509 </param>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
510 <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
511 <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
512 <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
513 <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
514 <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
515 </section>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
516 <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
517 <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
518 </section>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
519 <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
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 <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
522 <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
523 <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
524 <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
525 </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
526 <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
527 <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
528 <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
529 <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
530 <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
531 <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
532 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
533 <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
8
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
534 <test expect_num_outputs="10">
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
535 <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
536 <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
537 <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
538 <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
539 <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
540 </collection>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
541 </param>
8
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
542 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks_genotypes.tsv"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
543 <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
544 <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
545 <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
546 <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
547 </conditional>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
548 <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
549 <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
550 <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
551 </conditional>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
552 <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
553 <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
554 </conditional>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
555 <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
556 <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
557 <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
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 <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
565 </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
566 <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
567 <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
568 <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
569 <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
570 <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
571 <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
572 <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
8
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
573 <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary_wgenotypes.tsv"/>
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
574 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary_wgenotypes.tsv"/>
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
575 <output_collection name="out_fstats_popcompare" type="list" count="1">
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
576 <element name="parent-progeny" file="populations/populations.fst_parent-progeny.tsv" ftype="tabular"/>
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
577 </output_collection>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
578 </test>
4
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
579 <!-- 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
580 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
581 is used) -->
8
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
582 <test expect_num_outputs="10">
4
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
583 <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
584 <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
585 <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
586 <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
587 <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
588 </collection>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
589 </param>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
590 <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
591 <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
592 <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
593 </conditional>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
594 <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
595 <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
596 <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
597 </conditional>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
598 <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
599 <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
600 </conditional>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
601 <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
602 <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
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 <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
605 <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
606 <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
607 <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
608 <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
609 <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
610 <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
611 </assert_command>
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="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
613 <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
614 <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
615 <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
616 <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
617 <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
618 <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
619 <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
620 <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
8
564c33e5c3e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
iuc
parents: 6
diff changeset
621 <output_collection name="out_fstats_popcompare" type="list" count="0"/>
4
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
622 </test>
887cf585cafc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
iuc
parents: 3
diff changeset
623 <!-- 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
624 <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
625 <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
626 <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
627 <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
628 <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
629 <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
630 </collection>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
631 </param>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
632 <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
633 <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
634 <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
635 <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
636 <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
637 <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
638 <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
639 <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
640 </test>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
641 <!-- 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
642 <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
643 <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
644 <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
645 <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
646 <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
647 <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
648 </collection>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
649 </param>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
650 <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
651 <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
652 <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
653 <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
654 </section>
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 2
diff changeset
655 <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
656 <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
657 <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
658 <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
659 <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
660 <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
661 <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
662 <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
663 </test>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
664 </tests>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
665 <help>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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666 <![CDATA[
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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667 .. class:: infomark
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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668
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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669 **What it does**
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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670
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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671 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
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672
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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673 --------
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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674
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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675 **Input files**
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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676
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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677 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
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678
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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679 - Population map::
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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680
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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681 indv_01 1
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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682 indv_02 1
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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683 indv_03 1
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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684 indv_04 2
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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685 indv_05 2
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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686 indv_06 2
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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687
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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688
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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689 **Output files**
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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690
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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691 - XXX.tags.tsv file
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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692
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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693 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
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694
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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695 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
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696
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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697
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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698 - XXX.snps.tsv file
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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699
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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700 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
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701
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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702 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
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diff changeset
703
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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704
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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705 - 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
706
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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707 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
708
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 - 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
711
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
712 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
713
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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714 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
715
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
716
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
717 - other files:
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
718
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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719 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
720
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
721 @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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722 ]]>
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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723 </help>
3
b242deb58952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
724 <expand macro="citation"/>
0
6fba323a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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725 </tool>