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