Mercurial > repos > iuc > gemini_stats

annotate gemini_stats.xml @ 3:bfd828995cf7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:41:27 -0500
parents 544f687c4534
children ed118e624798
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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[
3
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12 @PROVIDE_ANNO_DATA@
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13
0
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14 gemini @BINARY@
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15 $stats_type
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16
3
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17 #set $multiline_sql_expr = $gt_filter
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18 #set $cmdln_param = "--gt-filter"
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19 @MULTILN_SQL_EXPR_TO_CMDLN@
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3
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21 #set $multiline_sql_expr = $summarize
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22 #set $cmdln_param = "--summarize"
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23 @MULTILN_SQL_EXPR_TO_CMDLN@
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25 "${ infile }"
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26 > "${ outfile }"
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27 ]]>
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28 </command>
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29 <inputs>
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30 <expand macro="infile" />
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31
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32 <param name="stats_type" type="select" label="Studying ..." help="">
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33 <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option>
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34 <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option>
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35 <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option>
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36 <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option>
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37 <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option>
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38 <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option>
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39 <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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40 <option value="--gts-by-sample">Return the count of each genotype class observed per sample (--gts-by-sample)</option>
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41 </param>
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42
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43 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">
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44 <expand macro="sanitize_query" />
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45 </param>
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47 <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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48 <expand macro="sanitize_query" />
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49 </param>
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50
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51 </inputs>
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52 <outputs>
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53 <data name="outfile" format="tabular" />
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
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58 <param name="stats_type" value="--vars-by-sample" />
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59 <output name="outfile" file="gemini_stats_result.tabular" />
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **What it does**
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64
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65 The stats tool computes some useful variant statistics for a GEMINI database.
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66 Like computing the transition and transversion ratios for the snps.
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67
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68 **Settings and examples**
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69
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70 --tstv-coding:
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71 Compute the transition/transversion ratios for the snps in the coding regions.
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72
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73 --tstv-noncoding:
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74 Compute the transition/transversion ratios for the snps in the non-coding regions.
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75
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76 EXAMPLE Compute the type and count of the snps; --snp-counts::
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78 type count
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79 A->G 2
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80 C->T 1
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81 G->A 1
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82
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83 EXAMPLE Calculate the site frequency spectrum of the variants; --sfs::
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84
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85 aaf count
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86 0.125 2
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87 0.375 1
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88
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89 EXAMPLE Compute the pair-wise genetic distance between each sample; --mds::
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90
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91 sample1 sample2 distance
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92 M10500 M10500 0.0
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93 M10475 M10478 1.25
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94 M10500 M10475 2.0
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95 M10500 M10478 0.5714
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96
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97 EXAMPLE Return a count of the types of genotypes per sample; --gts-by-sample::
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98
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99 sample num_hom_ref num_het num_hom_alt num_unknown total
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100 M10475 4 1 3 1 9
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101 M10478 2 2 4 1 9
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102
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103
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104
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105 EXAMPLE Return the total variants per sample (sum of homozygous and heterozygous variants); --vars-by-sample::
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106
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107 sample total
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108 M10475 4
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109 M10478 6
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110
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111 **Final solution**
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112
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113 --summarize:
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114 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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115
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116 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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117
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118 sample total num_het num_hom_alt
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119 M10475 1 1 0
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120 M128215 1 1 0
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121 M10478 2 2 0
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122 M10500 2 1 1
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123
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124
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125 ]]></help>
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126 <expand macro="citations"/>
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127 </tool>