[2] | 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** |
---|
| 34 | See GTOOL_ documentation link below for more details. Briefly, if |
---|
| 35 | your linkage format pedigree file has 1/2 in column 6 for control/case respectively, setting this to Yes will create two |
---|
| 36 | complete sets of output files distinguished by 1 and 2 respectively. otherwise, affection status is assumed to contain a |
---|
| 37 | continuous phenotype and a single output set is produced |
---|
| 38 | |
---|
| 39 | |
---|
| 40 | **Summary** |
---|
| 41 | |
---|
| 42 | Code 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** |
---|
| 49 | Originally designed and written for the Rgenetics |
---|
| 50 | series of Galaxy tools by ross lazarus (ross.lazarus@gmail.com), who didn't write GTOOL_ |
---|
| 51 | but wishes he had. |
---|
| 52 | |
---|
| 53 | </help> |
---|
| 54 | </tool> |
---|