Mercurial > repos > iuc > gemini_stats

annotate gemini_stats.xml @ 5:78e971dd87ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:28:45 -0500
parents ed118e624798
children c60ef99f03d3
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
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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@
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13 $stats_type
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14
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15 #set $multiline_sql_expr = $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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19 #set $multiline_sql_expr = $summarize
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20 #set $cmdln_param = "--summarize"
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21 @MULTILN_SQL_EXPR_TO_CMDLN@
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23 "${ infile }"
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24 > "${ outfile }"
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25 ]]>
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26 </command>
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27 <inputs>
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28 <expand macro="infile" />
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30 <param name="stats_type" type="select" label="Studying ..." help="">
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31 <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option>
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32 <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option>
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33 <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option>
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34 <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option>
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35 <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option>
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36 <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option>
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37 <option value="--vars-by-sample">Return the total variants per sample, sum of homozygous and heterozygous variants (--vars-by-sample)</option>
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38 <option value="--gts-by-sample">Return the count of each genotype class observed per sample (--gts-by-sample)</option>
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39 </param>
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40
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41 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">
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42 <expand macro="sanitize_query" />
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43 </param>
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44
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45 <param name="summarize" type="text" area="True" size="5x50" label="The query to be issued to the database to summarize" help="(--summarize)">
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46 <expand macro="sanitize_query" />
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47 </param>
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48 </inputs>
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49 <outputs>
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50 <data name="outfile" format="tabular" />
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51 </outputs>
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52 <tests>
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53 <test>
5
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54 <!-- test vars-by-sample report -->
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55 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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56 <param name="stats_type" value="--vars-by-sample" />
5
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57 <output name="outfile">
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58 <assert_contents>
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59 <has_line_matching expression="sample&#009;total" />
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60 </assert_contents>
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61 </output>
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62 </test>
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63 <test>
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64 <!-- test gts-by-sample report -->
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65 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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66 <param name="stats_type" value="--gts-by-sample" />
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67 <output name="outfile">
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68 <assert_contents>
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69 <has_line_matching expression="sample&#009;num_hom_ref&#009;num_het&#009;num_hom_alt&#009;num_unknown&#009;total" />
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70 </assert_contents>
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71 </output>
0
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 **What it does**
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77 The stats tool computes some useful variant statistics for a GEMINI database.
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78 Like computing the transition and transversion ratios for the snps.
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80 **Settings and examples**
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81
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82 --tstv-coding:
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83 Compute the transition/transversion ratios for the snps in the coding regions.
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84
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85 --tstv-noncoding:
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86 Compute the transition/transversion ratios for the snps in the non-coding regions.
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87
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88 EXAMPLE Compute the type and count of the snps; --snp-counts::
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89
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90 type count
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91 A->G 2
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92 C->T 1
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93 G->A 1
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94
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95 EXAMPLE Calculate the site frequency spectrum of the variants; --sfs::
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96
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97 aaf count
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98 0.125 2
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99 0.375 1
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100
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101 EXAMPLE Compute the pair-wise genetic distance between each sample; --mds::
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102
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103 sample1 sample2 distance
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104 M10500 M10500 0.0
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105 M10475 M10478 1.25
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106 M10500 M10475 2.0
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107 M10500 M10478 0.5714
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108
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109 EXAMPLE Return a count of the types of genotypes per sample; --gts-by-sample::
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110
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111 sample num_hom_ref num_het num_hom_alt num_unknown total
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112 M10475 4 1 3 1 9
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113 M10478 2 2 4 1 9
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114
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115
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116
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117 EXAMPLE Return the total variants per sample (sum of homozygous and heterozygous variants); --vars-by-sample::
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118
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119 sample total
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120 M10475 4
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121 M10478 6
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122
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123 **Final solution**
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124
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125 --summarize:
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126 If none of these tools are exactly what you want, you can summarize the variants per sample of an arbitrary query using the –summarize flag.
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127
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128 EXAMPLE If you wanted to know, for each sample, how many variants are on chromosome 1 that are also in dbSNP;--summarize "select * from variants where in_dbsnp=1 and chrom='chr1'"::
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129
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130 sample total num_het num_hom_alt
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131 M10475 1 1 0
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132 M128215 1 1 0
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133 M10478 2 2 0
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134 M10500 2 1 1
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135
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136
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137 ]]></help>
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138 <expand macro="citations"/>
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139 </tool>