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1 <tool id="rgQC1" name="QC reports:">
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2
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3 <description>Marker and Subject measures</description>
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4
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5 <command interpreter="python">
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6 rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$title"
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7 -s '$html_file' -p '$html_file.files_path'
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8 </command>
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9
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10 <inputs>
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11 <param name="input_file" type="data" label="RGenetics genotype file in compressed Plink format"
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12 size="80" format="pbed" />
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13 <param name="title" size="80" type="text" value="RgQC report" label="Descriptive report title"/>
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14 </inputs>
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15
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16 <outputs>
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17 <data format="html" name="html_file" metadata_source="input_file" label="${title}.html"/>
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18 </outputs>
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19
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20 <tests>
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21 <test>
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22 <param name='input_file' value='tinywga' ftype='pbed' >
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23 <metadata name='base_name' value='tinywga' />
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24 <composite_data value='tinywga.bim' />
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25 <composite_data value='tinywga.bed' />
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26 <composite_data value='tinywga.fam' />
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27 <edit_attributes type='name' value='tinywga' />
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28 </param>
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29 <param name='title' value='rgQCtest1' />
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30 <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='300'>
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31 <param name="dbkey" value="hg18" />
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32 <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "100000"/>
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33 <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/>
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34 <extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" />
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35 <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/>
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36 <extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" lines_diff="90"/>
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37 <extra_files type="file" name='tinywga.imendel' value="rgtestouts/rgQC/tinywga.imendel" compare="diff"/>
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38 <extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" />
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39 <extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" />
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40 <extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" />
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41 <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="sim_size" delta="100000"/>
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42 <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" lines_diff="10" />
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43 <extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="sim_size" delta="1000" />
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44 <extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" />
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45 <extra_files type="file" name='ldp_tinywga.log' value="rgtestouts/rgQC/ldp_tinywga.log" compare="diff" lines_diff="20"/>
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46 <extra_files type="file" name='Ranked_Marker_HWE.xls' value="rgtestouts/rgQC/Ranked_Marker_HWE.xls" compare="diff" />
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47 <extra_files type="file" name='Ranked_Marker_MAF.xls' value="rgtestouts/rgQC/Ranked_Marker_MAF.xls" compare="diff" />
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48 <extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" lines_diff="5"/>
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49 <extra_files type="file" name='Ranked_Subject_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls" compare="diff" lines_diff="40"/>
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50 <extra_files type="file" name='tinywga_fracmiss_cum.jpg' value="rgtestouts/rgQC/tinywga_fracmiss_cum.jpg" compare="sim_size" delta = "20000"/>
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51 <extra_files type="file" name='tinywga_fracmiss_cum.pdf' value="rgtestouts/rgQC/tinywga_fracmiss_cum.pdf" compare="sim_size" delta = "100000"/>
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52 </output>
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53 </test>
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54 </tests>
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55 <help>
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56
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57 .. class:: infomark
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58
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59 **Summary**
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60
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61 This tool prepares an extensive and comprehensive series of reports for quality control checking of SNP genotypes from any arbitrary
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62 genotyping experiment. Designed for family based data, so includes optional reports on Mendelian errors by
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63 subject and by marker.
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64
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65 The outputs include histograms and boxplots for missingness, maf, mendel counts and hwe by marker, and the ones that make sense by
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66 subject. The report is built as a single web page containing links to the summary marker and subject files.
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67
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68 The F (inbreeding) statistic is calculated using a somewhat LD independent group of genotypes
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69 The Plink used is --indep-pairwise 40 20 0.5 until we make it configurable.
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70 High heterozygosity might mean contaminated sample - more than one DNA. Low heterozygosity might mean inbreeding as in strains
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71 of mice.
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72
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73 If the data file you want is missing from the option list above,
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74 you will first need to "import" it so it will be available here. Files available in the system library
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75 can be imported by selecting and completing the "Import ped/map" choice from the Get Data tool group at the top of the Galaxy
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76 menu. Your system administrator will be responsible for adding files to the system library.
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77
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78 -----
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79
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80 .. class:: infomark
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81
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82 **Syntax**
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83
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84 - **Genotype file** is the input pedfile -
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85 - **Prefix** is a string used to name all of the outputs
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86
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87 -----
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88
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89 **Attribution**
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90
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91 This Galaxy tool was written by Ross Lazarus for the Rgenetics project
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92 The current version uses Plink for most calculations and R for plotting - for full Plink attribution, source code and documentation,
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93 please see http://pngu.mgh.harvard.edu/~purcell/plink/ while R attribution and source code can be found at http://r-project.org
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94
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95 Shaun Purcell provides the documentation you need specific to those settings, at
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96 http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#glm
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97
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98 Tool and Galaxy datatypes originally designed and written for the Rgenetics
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99 series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus@gmail.com)
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100 Shaun Purcell created and maintains Plink, while a cast of many maintain R.
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101
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102 Please acknowledge your use of this tool, Galaxy, R and Plink in your publications and let
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103 us know so we can keep track. These tools all rely on highly competitive grant funding
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104 so your letting us know about publications is important to our ongoing support.
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105
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106 </help>
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107
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108
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109
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110 </tool>
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