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annotate gemini_stats.xml @ 5:86d4303cc3ca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:43:48 -0500
parents cdd90678004a
children b92cfa44f5be
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5
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>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">stats</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 gemini @BINARY@
5
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13 #if str($stats.type) == "gts-stats":
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14 #set $multiline_sql_expr = $stats.variants.gt_filter
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15 #set $cmdln_param = "--gt-filter"
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16 @MULTILN_SQL_EXPR_TO_CMDLN@
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17
5
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18 #if str($stats.variants.constraint).strip():
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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19 #set $multiline_sql_expr = "select * from variants WHERE " + str($stats.variants.constraint)
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20 #else:
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21 #set $multiline_sql_expr = "select * from variants"
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22 #end if
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23 #set $cmdln_param = "--summarize"
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24 @MULTILN_SQL_EXPR_TO_CMDLN@
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25 #else:
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26 ${stats.stats_option}
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27 #end if
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28 '$infile'
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29 > '$outfile'
0
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30 ]]>
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31 </command>
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32 <inputs>
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33 <expand macro="infile" />
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34
5
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35 <conditional name="stats">
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36 <param name="type" type="select"
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37 label="Select the type of statistics you are interested in" help="">
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38 <option value="gts-stats">Genotype counts tabulated by sample (--summarize)</option>
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39 <option value="snp-counts">Counts of SNPs by nucleotide change (--snp-counts)</option>
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40 <option value="tstv-stats">Transition / transversion statistics for the SNPs in the dataset</option>
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41 <option value="aaf">Alternate allele frequency spectrum of all variants (--sfs)</option>
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42 <option value="sample-distance">Pair-wise genetic distances between for all samples (--mds)</option>
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43 </param>
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44 <when value="snp-counts">
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45 <param name="stats_option" type="hidden" value="--snp-counts" />
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46 </when>
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47 <when value="aaf">
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48 <param name="stats_option" type="hidden" value="--sfs" />
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49 </when>
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50 <when value="sample-distance">
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51 <param name="stats_option" type="hidden" value="--mds" />
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52 </when>
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53 <when value="tstv-stats">
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54 <param name="stats_option" type="select"
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55 label="Calculate Ts/Tv statistics based on"
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56 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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57 <option value="--tstv">All SNPs (--tstv)</option>
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58 <option value="--tstv-coding">SNPs in coding regions (--tstv-coding)</option>
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59 <option value="--tstv-noncoding">SNPs in non-coding regions (--tstv-noncoding)</option>
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60 </param>
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61 </when>
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62 <when value="gts-stats">
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63 <param name="stats_option" type="hidden" value="" />
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64 <conditional name="variants">
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65 <param name="keep" type="select"
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66 label="Compute the genotype counts table based on"
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67 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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68 <option value="all">All variants</option>
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69 <option value="custom">Custom filtered variants</option>
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70 </param>
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71 <when value="all">
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72 <param name="gt_filter" type="hidden" value="" />
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73 <param name="constraint" type="hidden" value="" />
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74 </when>
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75 <when value="custom">
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76 <param argument="--gt-filter" name="gt_filter" type="text" area="True" size="5x50"
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77 label="Restrictions to apply to genotype values"
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78 help="">
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79 <expand macro="sanitize_query" />
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80 </param>
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81 <param name="constraint" type="text" area="True" size="5x50"
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82 label="Additional constraints on the variants"
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83 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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84 <expand macro="sanitize_query" />
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85 </param>
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86 </when>
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87 </conditional>
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88 </when>
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89 </conditional>
0
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90 </inputs>
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91 <outputs>
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92 <data name="outfile" format="tabular" />
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93 </outputs>
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94 <tests>
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95 <test>
4
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96 <!-- test vars-by-sample report -->
5
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97 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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98 <conditional name="stats">
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99 <param name="type" value="tstv-stats" />
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100 <param name="stats_option" value="--tstv-coding" />
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101 </conditional>
4
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102 <output name="outfile">
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103 <assert_contents>
5
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104 <!-- since the input file is not annotated
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105 no variants will be considered to be in coding regions -->
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106 <has_line line="ts&#009;tv&#009;ts/tv" />
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107 <has_line line="0&#009;0&#009;0" />
4
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <test>
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112 <!-- test gts-by-sample report -->
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113 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
5
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114 <conditional name="stats">
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115 <param name="type" value="gts-stats" />
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116 <conditional name="variants">
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117 <param name="keep" value="all" />
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118 </conditional>
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119 </conditional>
4
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120 <output name="outfile">
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121 <assert_contents>
5
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122 <has_line_matching expression="sample&#009;total&#009;num_het&#009;num_hom_alt&#009;num_hom_ref" />
4
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123 </assert_contents>
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124 </output>
0
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125 </test>
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126 </tests>
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127 <help><![CDATA[
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128 **What it does**
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129
5
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130 The stats tool computes one of the following useful variant statistics for a GEMINI database:
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131
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132 **Genotype counts tabulated by sample**:
0
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133
5
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134 This mode uses the ``gemini stats --summarize`` option to produce a table with
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135 one row per sample, which tabulates the numbers of sites, for which a given
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136 sample shows a:
0
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137
5
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138 - non-reference genotype (*total* column; the sum of the *num_het* and *num_hom_alt* columns next to it)
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139 - heterozygous genotype (*num_het* column)
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140 - homozygous variant genotype (*num_hom_alt* column)
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141 - homozygous reference genotype (*num_hom_ref* column)
0
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142
5
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143 You can choose to calculate the table based on all variants in your database,
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144 or to filter the variants before the calculation using GEMINI genotype filter
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145 expressions and/or WHERE clauses of GEMINI queries.
0
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146
5
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147 **Counts of SNPs by nucleotide change**:
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148
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149 This runs ``gemini stats`` with the ``--snp-count`` option. The result is a
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150 simple table listing the number of occurences of each observed REF->ALT change
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151 in your database, e.g.::
0
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152
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153 type count
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154 A->G 2
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155 C->T 1
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156 G->A 1
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157
5
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158 **Transition / transversion statistics**
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159
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160 This mode uses ``gemini stats`` with the ``--tstv``, ``--tstv-coding``, or
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161 ``--tstv-noncoding`` option to compute the transition/transversion ratios for
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162 all SNPs, for SNPs in coding, or SNPs in non-coding regions, respectively.
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163
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164 The result is presented in a 1x3 table listing the number of
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165 transitions (*ts* column), transversions (*tv* column) and the ratio of the two
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166 (*ts/tv* column), e.g.::
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167
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168 ts tv ts/tv
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169 126 39 3.2307
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170
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171 **Alternate allele frequency spectrum**
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172
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173 Runs ``gemini stats --sfs`` to produce binned alternate allele frequency counts
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174 in a table like::
0
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175
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176 aaf count
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177 0.125 2
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178 0.375 1
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179
5
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180 **Pairwise genetic distances**
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181
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182 Runs ``gemini stats --mds`` and tabulates all pairwise genetic distance for the
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iuc
parents: 4
diff changeset
183 samples in your database. An example could look like this::
0
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
184
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
185 sample1 sample2 distance
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
186 M10500 M10500 0.0
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
187 M10475 M10478 1.25
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
188 M10500 M10475 2.0
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
189 M10500 M10478 0.5714
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
190
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
191 ]]></help>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
192 <expand macro="citations"/>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
193 </tool>