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annotate gemini_stats.xml @ 8:b92cfa44f5be draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:31:49 +0000
parents 86d4303cc3ca
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86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
0
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2 <description>Compute useful variant statistics</description>
8
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">stats</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 gemini @BINARY@
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14 #if str($stats.type) == "gts-stats":
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15 #set $multiline_sql_expr = $stats.variants.gt_filter
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16 #set $cmdln_param = "--gt-filter"
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17 @MULTILN_SQL_EXPR_TO_CMDLN@
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18
5
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19 #if str($stats.variants.constraint).strip():
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20 #set $multiline_sql_expr = "select * from variants WHERE " + str($stats.variants.constraint)
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21 #else:
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22 #set $multiline_sql_expr = "select * from variants"
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23 #end if
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24 #set $cmdln_param = "--summarize"
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25 @MULTILN_SQL_EXPR_TO_CMDLN@
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26 #else:
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27 ${stats.stats_option}
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28 #end if
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29 '$infile'
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30 > '$outfile'
0
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31 ]]>
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32 </command>
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33 <inputs>
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34 <expand macro="infile" />
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35
5
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36 <conditional name="stats">
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37 <param name="type" type="select"
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38 label="Select the type of statistics you are interested in" help="">
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39 <option value="gts-stats">Genotype counts tabulated by sample (--summarize)</option>
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40 <option value="snp-counts">Counts of SNPs by nucleotide change (--snp-counts)</option>
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41 <option value="tstv-stats">Transition / transversion statistics for the SNPs in the dataset</option>
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42 <option value="aaf">Alternate allele frequency spectrum of all variants (--sfs)</option>
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43 <option value="sample-distance">Pair-wise genetic distances between for all samples (--mds)</option>
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44 </param>
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45 <when value="snp-counts">
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46 <param name="stats_option" type="hidden" value="--snp-counts" />
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47 </when>
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48 <when value="aaf">
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49 <param name="stats_option" type="hidden" value="--sfs" />
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50 </when>
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51 <when value="sample-distance">
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52 <param name="stats_option" type="hidden" value="--mds" />
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53 </when>
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54 <when value="tstv-stats">
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55 <param name="stats_option" type="select"
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56 label="Calculate Ts/Tv statistics based on"
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57 help="Restricting the calculation to coding/noncoding regions will only produce meaningful results with preannotated variants. If you haven't annotated your variants with SnpEff or VEP before loading them into GEMINI, select All SNPs.">
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58 <option value="--tstv">All SNPs (--tstv)</option>
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59 <option value="--tstv-coding">SNPs in coding regions (--tstv-coding)</option>
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60 <option value="--tstv-noncoding">SNPs in non-coding regions (--tstv-noncoding)</option>
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61 </param>
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62 </when>
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63 <when value="gts-stats">
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64 <param name="stats_option" type="hidden" value="" />
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65 <conditional name="variants">
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66 <param name="keep" type="select"
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67 label="Compute the genotype counts table based on"
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68 help="If you select All variants the genotype counts will be produced using --summarize with the wildcard query &quot;select * from variants&quot;.">
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69 <option value="all">All variants</option>
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70 <option value="custom">Custom filtered variants</option>
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71 </param>
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72 <when value="all">
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73 <param name="gt_filter" type="hidden" value="" />
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74 <param name="constraint" type="hidden" value="" />
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75 </when>
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76 <when value="custom">
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77 <param argument="--gt-filter" name="gt_filter" type="text" area="True" size="5x50"
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78 label="Restrictions to apply to genotype values"
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79 help="">
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80 <expand macro="sanitize_query" />
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81 </param>
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82 <param name="constraint" type="text" area="True" size="5x50"
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83 label="Additional constraints on the variants"
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84 help="Enter valid constraints for the WHERE clause of a GEMINI query here. You could use, for example: chrom = 'chr1' or impact_severity = 'HIGH', to include only high-impact variants on chromosome 1 in the counts table.">
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85 <expand macro="sanitize_query" />
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86 </param>
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87 </when>
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88 </conditional>
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89 </when>
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90 </conditional>
0
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91 </inputs>
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92 <outputs>
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93 <data name="outfile" format="tabular" />
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94 </outputs>
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95 <tests>
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96 <test>
4
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97 <!-- test vars-by-sample report -->
5
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98 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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99 <conditional name="stats">
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100 <param name="type" value="tstv-stats" />
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101 <param name="stats_option" value="--tstv-coding" />
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102 </conditional>
4
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103 <output name="outfile">
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104 <assert_contents>
5
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105 <!-- since the input file is not annotated
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106 no variants will be considered to be in coding regions -->
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107 <has_line line="ts&#009;tv&#009;ts/tv" />
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108 <has_line line="0&#009;0&#009;0" />
4
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109 </assert_contents>
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110 </output>
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111 </test>
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112 <test>
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113 <!-- test gts-by-sample report -->
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114 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
5
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115 <conditional name="stats">
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116 <param name="type" value="gts-stats" />
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117 <conditional name="variants">
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118 <param name="keep" value="all" />
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119 </conditional>
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120 </conditional>
4
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121 <output name="outfile">
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122 <assert_contents>
5
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123 <has_line_matching expression="sample&#009;total&#009;num_het&#009;num_hom_alt&#009;num_hom_ref" />
4
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124 </assert_contents>
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125 </output>
0
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126 </test>
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127 </tests>
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128 <help><![CDATA[
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129 **What it does**
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130
5
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131 The stats tool computes one of the following useful variant statistics for a GEMINI database:
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132
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133 **Genotype counts tabulated by sample**:
0
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134
5
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135 This mode uses the ``gemini stats --summarize`` option to produce a table with
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136 one row per sample, which tabulates the numbers of sites, for which a given
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137 sample shows a:
0
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138
5
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139 - non-reference genotype (*total* column; the sum of the *num_het* and *num_hom_alt* columns next to it)
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140 - heterozygous genotype (*num_het* column)
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141 - homozygous variant genotype (*num_hom_alt* column)
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142 - homozygous reference genotype (*num_hom_ref* column)
0
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143
5
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144 You can choose to calculate the table based on all variants in your database,
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145 or to filter the variants before the calculation using GEMINI genotype filter
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146 expressions and/or WHERE clauses of GEMINI queries.
0
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147
5
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148 **Counts of SNPs by nucleotide change**:
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149
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150 This runs ``gemini stats`` with the ``--snp-count`` option. The result is a
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151 simple table listing the number of occurences of each observed REF->ALT change
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152 in your database, e.g.::
0
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153
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154 type count
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155 A->G 2
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156 C->T 1
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157 G->A 1
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158
5
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159 **Transition / transversion statistics**
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160
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161 This mode uses ``gemini stats`` with the ``--tstv``, ``--tstv-coding``, or
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162 ``--tstv-noncoding`` option to compute the transition/transversion ratios for
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163 all SNPs, for SNPs in coding, or SNPs in non-coding regions, respectively.
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164
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165 The result is presented in a 1x3 table listing the number of
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166 transitions (*ts* column), transversions (*tv* column) and the ratio of the two
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167 (*ts/tv* column), e.g.::
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168
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169 ts tv ts/tv
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170 126 39 3.2307
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171
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172 **Alternate allele frequency spectrum**
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173
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174 Runs ``gemini stats --sfs`` to produce binned alternate allele frequency counts
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175 in a table like::
0
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176
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177 aaf count
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178 0.125 2
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179 0.375 1
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180
5
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181 **Pairwise genetic distances**
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182
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183 Runs ``gemini stats --mds`` and tabulates all pairwise genetic distance for the
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184 samples in your database. An example could look like this::
0
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185
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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186 sample1 sample2 distance
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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187 M10500 M10500 0.0
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188 M10475 M10478 1.25
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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189 M10500 M10475 2.0
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190 M10500 M10478 0.5714
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191
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192 ]]></help>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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193 <expand macro="citations"/>
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194 </tool>