Mercurial > repos > xuebing > sharplabtool
comparison tools/rgenetics/rgGTOOL.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="rgGTOOL1" name="Converter"> | |
| 2 | |
| 3 | |
| 4 <description>from linkage format to SNPTEST Marchini files</description> | |
| 5 | |
| 6 <command interpreter="python"> | |
| 7 rgGTOOL.py $i $o $discrete $logf $outdir | |
| 8 </command> | |
| 9 | |
| 10 <inputs> | |
| 11 <param name="i" type="select" label="Genotype file" dynamic_options="get_lib_pedfiles()" /> | |
| 12 <param name="discrete" type="select" label="Make Case/Control based on affection 2/1"> | |
| 13 <option selected="yes" value="1">Discrete</option> | |
| 14 <option value="0">Continuous</option> | |
| 15 </param> | |
| 16 <param name="o" type="text" label="Output Marchini format name" value="Marchini"/> | |
| 17 <param name="outdir" type="hidden" value="/usr/local/galaxy/data/rg/snptest" /> | |
| 18 </inputs> | |
| 19 | |
| 20 <outputs> | |
| 21 <data format="txt" name="logf" /> | |
| 22 </outputs> | |
| 23 <help> | |
| 24 | |
| 25 | |
| 26 **Syntax** | |
| 27 | |
| 28 - **Genotype file** is the input linkage format pedigree and corresponding map file | |
| 29 - **Discrete** is the type of phenotype in the affection column | |
| 30 - **Output name** is the file name (.gen and .sample will be added) for the new SNPTEST compatible file | |
| 31 | |
| 32 **Note on Discrete** | |
| 33 See GTOOL_ documentation link below for more details. Briefly, if | |
| 34 your linkage format pedigree file has 1/2 in column 6 for control/case respectively, setting this to Yes will create two | |
| 35 complete sets of output files distinguished by 1 and 2 respectively. otherwise, affection status is assumed to contain a | |
| 36 continuous phenotype and a single output set is produced | |
| 37 | |
| 38 | |
| 39 **Summary** | |
| 40 | |
| 41 Code used here from Jonathon Marchini's group - see documentation at GTOOL_. | |
| 42 | |
| 43 .. _GTOOL: http://www.stats.ox.ac.uk/~marchini/software/gwas/gtool.html | |
| 44 | |
| 45 ----- | |
| 46 | |
| 47 **Attribution** | |
| 48 Originally designed and written for the Rgenetics | |
| 49 series of Galaxy tools by ross lazarus (ross.lazarus@gmail.com), who didn't write GTOOL_ | |
| 50 but wishes he had. | |
| 51 | |
| 52 </help> | |
| 53 </tool> |