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

<tool id="rgEigPCA1" name="Eigensoft:">
    <code file="rgEigPCA_code.py"/>
    <description>PCA Ancestry using SNP</description>

    <command interpreter="python">
    rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
    "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca"
    </command>

    <inputs>

       <param name="i"  type="data" label="Input genotype data file"
          size="120" format="ldindep" />
       <param name="title"  type="text" value="Ancestry PCA" label="Title for outputs from this run"
          size="80"  />
       <param name="k"  type="integer" value="4" label="Number of principal components to output"
          size="3"  />
       <param name="m"  type="integer" value="0" label="Max. outlier removal iterations"
          help="To turn on outlier removal, set m=5 or so. Do this if you plan on adjusting any analyses"
          size="3"  />
       <param name="t"  type="integer" value="5" label="# principal components used for outlier removal"
          size="3"  />
       <param name="s"  type="integer" value="6" label="#SDs for outlier removal"
          help = "Any individual with SD along one of k top principal components > s will be removed as an outlier."
          size="3"  />

   </inputs>

   <outputs>
       <data name="out_file1" format="html" />
       <data name="pca" format="txt" />
   </outputs>

<!-- python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/pca.out $BINPATH -->

<tests>
 <test>
   <param name='i' value='tinywga' ftype='ldindep' >
   <metadata name='base_name' value='tinywga' />
   <composite_data value='tinywga.bim' />
   <composite_data value='tinywga.bed' />
   <composite_data value='tinywga.fam' />
   <edit_attributes type='name' value='tinywga' /> 
   </param>
    <param name='title' value='rgEigPCAtest1' />
    <param name="k" value="4" />
    <param name="m" value="2" />
    <param name="t" value="2" />
    <param name="s" value="2" />
    <output name='out_file1' file='rgtestouts/rgEigPCA/rgEigPCAtest1.html' ftype='html' compare='diff' lines_diff='195'>
    <extra_files type="file" name='rgEigPCAtest1_PCAPlot.pdf' value="rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf" compare="sim_size" delta="3000"/>
    </output>
    <output name='pca' file='rgtestouts/rgEigPCA/rgEigPCAtest1.txt' compare='diff'/>
 </test>
</tests>

<help>


**Syntax**

- **Genotype data** is the input genotype file chosen from available library files.
- **Title** is used to name the output files
- **Tuning parameters** documented in the Eigensoft documentation - see below

(Note that you may need to convert an existing genotype file into that format to use this tool)

-----

**Summary**

**Attribution**
This tool runs and relies on the work of many others, including the
maintainers of the Eigensoft program, and the R and
Bioconductor projects. For full attribution, source code and documentation, please see
http://genepath.med.harvard.edu/~reich/Software.htm, http://cran.r-project.org/
and http://www.bioconductor.org/ respectively

This implementation is a Galaxy tool wrapper around these third party applications.
It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit.

copyright Ross Lazarus 2007
Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html
but is about as useful as a sponge boat without EIGENSOFT pca code.

**README from eigensoft2**

[rerla@beast eigensoft2]$ cat README
EIGENSOFT version 2.0, January 2008 (for Linux only)

This is the same as our EIGENSOFT 2.0 BETA release with a few recent changes
as described at http://genepath.med.harvard.edu/~reich/New_In_EIGENSOFT.htm.

Features of EIGENSOFT version 2.0 include:
-- Keeping track of ref/var alleles in all file formats: see CONVERTF/README
-- Handling data sets up to 8 billion genotypes: see CONVERTF/README
-- Output SNP weightings of each principal component: see POPGEN/README

The EIGENSOFT package implements methods from the following 2 papers:
Patterson N. et al. 2006 PLoS Genetics in press (population structure)
Price A.L. et al. 2006 NG 38:904-9 (EIGENSTRAT stratification correction)

See POPGEN/README for documentation of population structure programs.

See EIGENSTRAT/README for documentation of EIGENSTRAT programs.

See CONVERTF/README for documentation of programs for converting file formats.


Executables and source code:
----------------------------
All C executables are in the bin/ directory.

We have placed source code for all C executables in the src/ directory,
for users who wish to modify and recompile our programs.  For example, to
recompile the eigenstrat program, type
"cd src"
"make eigenstrat"
"mv eigenstrat ../bin"

Note that some of our software will only compile if your system has the
lapack package installed.  (This package is used to compute eigenvectors.)
Some users may need to change "blas-3" to "blas" in the Makefile,
depending on how blas and lapack are installed.

If cc is not available on your system, try "cp Makefile.alt Makefile"
and then recompile.

If you have trouble compiling and running our code, try compiling and
running the pcatoy program in the src directory:
"cd src"
"make pcatoy"
"./pcatoy"
If you are unable to run the pcatoy program successfully, please contact
your system administrator for help, as this is a systems issue which is
beyond our scope.  Your system administrator will be able to troubleshoot
your systems issue using this trivial program.  [You can also try running
the pcatoy program in the bin directory, which we have already compiled.]
</help>
</tool>