root/galaxy-central/tools/rgenetics/rgGTOOL.xml

リビジョン 2, 1.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="rgGTOOL1" name="Converter">
2    <code file="listFiles.py"/>
3    <code file="rgGTOOL_code.py"/>
4 
5    <description>from linkage format to SNPTEST Marchini files</description>
6 
7    <command interpreter="python">
8        rgGTOOL.py $i $o $discrete $logf $outdir
9    </command>
10   
11    <inputs>   
12       <param name="i"  type="select" label="Genotype file" dynamic_options="get_lib_pedfiles()" />
13       <param name="discrete" type="select" label="Make Case/Control based on affection 2/1">
14                        <option selected="yes" value="1">Discrete</option>
15                        <option value="0">Continuous</option>
16       </param>
17       <param name="o" type="text" label="Output Marchini format name" value="Marchini"/>
18       <param name="outdir" type="hidden" value="/usr/local/galaxy/data/rg/snptest" />
19   </inputs>
20
21   <outputs> 
22       <data format="txt" name="logf"  />
23   </outputs>
24<help>
25
26
27**Syntax**
28
29- **Genotype file** is the input linkage format pedigree and corresponding map file
30- **Discrete** is the type of phenotype in the affection column
31- **Output name** is the file name (.gen and .sample will be added) for the new SNPTEST compatible file
32
33**Note on Discrete**
34See GTOOL_ documentation link below for more details. Briefly, if
35your linkage format pedigree file has 1/2 in column 6 for control/case respectively, setting this to Yes will create two
36complete sets of output files distinguished by 1 and 2 respectively. otherwise, affection status is assumed to contain a
37continuous phenotype and a single output set is produced
38
39
40**Summary**
41
42Code used here from Jonathon Marchini's group - see documentation at GTOOL_.
43
44.. _GTOOL: http://www.stats.ox.ac.uk/~marchini/software/gwas/gtool.html
45
46-----
47
48**Attribution**
49Originally designed and written for the Rgenetics
50series of Galaxy tools by ross lazarus (ross.lazarus@gmail.com), who didn't write GTOOL_
51but wishes he had.
52
53</help>
54</tool>
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