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comparison tools/rgenetics/rgQC.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="rgQC1" name="QC reports:">
2
3 <description>Marker and Subject measures</description>
4
5 <command interpreter="python">
6 rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$title"
7 -s '$html_file' -p '$html_file.files_path'
8 </command>
9
10 <inputs>
11 <param name="input_file" type="data" label="RGenetics genotype file in compressed Plink format"
12 size="80" format="pbed" />
13 <param name="title" size="80" type="text" value="RgQC report" label="Descriptive report title"/>
14 </inputs>
15
16 <outputs>
17 <data format="html" name="html_file" metadata_source="input_file" label="${title}.html"/>
18 </outputs>
19
20 <tests>
21 <test>
22 <param name='input_file' value='tinywga' ftype='pbed' >
23 <metadata name='base_name' value='tinywga' />
24 <composite_data value='tinywga.bim' />
25 <composite_data value='tinywga.bed' />
26 <composite_data value='tinywga.fam' />
27 <edit_attributes type='name' value='tinywga' />
28 </param>
29 <param name='title' value='rgQCtest1' />
30 <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='300'>
31 <param name="dbkey" value="hg18" />
32 <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "100000"/>
33 <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/>
34 <extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" />
35 <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/>
36 <extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" lines_diff="90"/>
37 <extra_files type="file" name='tinywga.imendel' value="rgtestouts/rgQC/tinywga.imendel" compare="diff"/>
38 <extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" />
39 <extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" />
40 <extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" />
41 <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="sim_size" delta="100000"/>
42 <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" lines_diff="10" />
43 <extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="sim_size" delta="1000" />
44 <extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" />
45 <extra_files type="file" name='ldp_tinywga.log' value="rgtestouts/rgQC/ldp_tinywga.log" compare="diff" lines_diff="20"/>
46 <extra_files type="file" name='Ranked_Marker_HWE.xls' value="rgtestouts/rgQC/Ranked_Marker_HWE.xls" compare="diff" />
47 <extra_files type="file" name='Ranked_Marker_MAF.xls' value="rgtestouts/rgQC/Ranked_Marker_MAF.xls" compare="diff" />
48 <extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" lines_diff="5"/>
49 <extra_files type="file" name='Ranked_Subject_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls" compare="diff" lines_diff="40"/>
50 <extra_files type="file" name='tinywga_fracmiss_cum.jpg' value="rgtestouts/rgQC/tinywga_fracmiss_cum.jpg" compare="sim_size" delta = "20000"/>
51 <extra_files type="file" name='tinywga_fracmiss_cum.pdf' value="rgtestouts/rgQC/tinywga_fracmiss_cum.pdf" compare="sim_size" delta = "100000"/>
52 </output>
53 </test>
54 </tests>
55 <help>
56
57 .. class:: infomark
58
59 **Summary**
60
61 This tool prepares an extensive and comprehensive series of reports for quality control checking of SNP genotypes from any arbitrary
62 genotyping experiment. Designed for family based data, so includes optional reports on Mendelian errors by
63 subject and by marker.
64
65 The outputs include histograms and boxplots for missingness, maf, mendel counts and hwe by marker, and the ones that make sense by
66 subject. The report is built as a single web page containing links to the summary marker and subject files.
67
68 The F (inbreeding) statistic is calculated using a somewhat LD independent group of genotypes
69 The Plink used is --indep-pairwise 40 20 0.5 until we make it configurable.
70 High heterozygosity might mean contaminated sample - more than one DNA. Low heterozygosity might mean inbreeding as in strains
71 of mice.
72
73 If the data file you want is missing from the option list above,
74 you will first need to "import" it so it will be available here. Files available in the system library
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
76 menu. Your system administrator will be responsible for adding files to the system library.
77
78 -----
79
80 .. class:: infomark
81
82 **Syntax**
83
84 - **Genotype file** is the input pedfile -
85 - **Prefix** is a string used to name all of the outputs
86
87 -----
88
89 **Attribution**
90
91 This Galaxy tool was written by Ross Lazarus for the Rgenetics project
92 The current version uses Plink for most calculations and R for plotting - for full Plink attribution, source code and documentation,
93 please see http://pngu.mgh.harvard.edu/~purcell/plink/ while R attribution and source code can be found at http://r-project.org
94
95 Shaun Purcell provides the documentation you need specific to those settings, at
96 http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#glm
97
98 Tool and Galaxy datatypes originally designed and written for the Rgenetics
99 series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus@gmail.com)
100 Shaun Purcell created and maintains Plink, while a cast of many maintain R.
101
102 Please acknowledge your use of this tool, Galaxy, R and Plink in your publications and let
103 us know so we can keep track. These tools all rely on highly competitive grant funding
104 so your letting us know about publications is important to our ongoing support.
105
106 </help>
107
108
109
110 </tool>