<tool id="fakePhe1" name="Null phenotypes">
  <description>for testing</description>
   <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
   "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
   </command>
   <inputs>
    <page>
    <param name="infile1"
         type="data" format="pbed,lped"
         label="Pedigree from Dataset" />
        <param name="title1" type="text"
         value="My null phenos" size="60"
         label="Title for outputs"/>
        <param name="dbkey" type="hidden" value='hg18' />
    </page>
    <page>
    <repeat name="fakePhe" title="Phenotypes to simulate under the Null">
        <param name="pName" type="text" label="Phenotype Name">
        </param>
      <conditional name="series">
        <param name="phetype" type="select" label="Phenotype Distribution">
          <option value="rnorm" selected="true">Random Normal variate</option>
          <option value="unif">Random Uniform variate</option>
          <option value="rgamma">Random Gamma variate</option>
          <option value="weibull">Random Weibull variate</option>
          <option value="exponential">Random exponential variate</option>
          <option value="poisson">Random Poisson variate</option>
          <option value="cat">Random categorical choice</option>
        </param>
        <when value="poisson">
          <param name="lamb" type="integer" value="2" label="Lambda (mean and variance)" />
        </when>
        <when value="rnorm">
          <param name="Mean" type="float" value="0.0" label="Mean" />
          <param name="SD" type="float" label="SD" value="1.0"/>
        </when>
        <when value="exponential">
          <param name="Mean" type="float" value="1.0" label="Mean" help="lambda for the exponential will be 1.0/Mean" />=
        </when>
        <when value="rgamma">
          <param name="Alpha" type="float" value="10" label="Alpha">
          </param>
          <param name="Beta" type="float" label="Beta" value="1.0">
          </param>
        </when>
        <when value="weibull">
          <param name="Alpha" type="float" value="10" label="Alpha">
          </param>
          <param name="Beta" type="float" label="Beta" value="1.0">
          </param>
        </when>
        <when value="unif">
          <param name="low" type="float" value="0.0" label="Lowest uniform value">
          </param>
          <param name="hi" type="float" label="Highest uniform value" value="1.0"
           help="A uniform value will be generated from the range specified (low to high) - eg 0.0 to 1.0">
          </param>
        </when>
        <when value="cat">
          <param name="values" type="text" value="A,B,C" label="Comma separated values to choose from"
         help = "Each of the comma separated values will have an equal probability of being chosen - eg 'A1,A2,B1,B2'">
          </param>
        </when>
      </conditional>
    </repeat>
    </page>
</inputs>
<outputs>
       <data format="pphe" name="ppheout"  metadata_source="infile1" />
</outputs>
<configfiles>
<configfile name="script_file">
#for $n, $f in enumerate($fakePhe)
#if $f.series.phetype=='rnorm'
{'pN':'$f.pName','pT':'rnorm','pP':"{'Mean':'$f.series.Mean', 'SD':'$f.series.SD'}"}
#elif $f.series.phetype=='rgamma'
{'pN':'$f.pName','pT':'rgamma','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"}
#elif $f.series.phetype=='poisson'
{'pN':'$f.pName','pT':'poisson','pP':"{'lamb':'$f.series.lamb',}"}
#elif $f.series.phetype=='exponential'
{'pN':'$f.pName','pT':'exponential','pP':"{'Mean':'$f.series.Mean',}"}
#elif $f.series.phetype=='weibull'
{'pN':'$f.pName','pT':'weibull','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"}
#elif $f.series.phetype=='cat'
{'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'values':'$f.series.values'}"}
#elif $f.series.phetype=='unif'
{'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'low':'$f.series.low','hi':'$f.series.hi'}"}
#end if
#end for
</configfile>
</configfiles>
<help>
.. class:: infomark

This tool allows you to generate an arbitrary (sort of)
synthetic phenotype file with measurements drawn from normal,
gamma, weibull, exponential, uniform or categorical distributions. These are for testing under
the null hypothesis of no association - the values are random but
from user specified distributions.

Two output files will appear - one for FBAT and the other for Plink since unfortunately,
they have slightly differing requirements for the header row.

-----

.. class:: warningmark

This tool is very experimental

-----

- **Pedigree** is a library pedigree file - the id's will be used in the synthetic null phenotypes
- **Title** is a name to give to the output phenotype file

On the next page, you can add an unlimited number of various kinds of phenotypes including choices for
categorical ones or distributions with specific parameters

Just keep using the "Add new phenotype" button to add new specifications until you're done.
Use the Execute button to run the program and generate the null phenotype data.
The new files will be available on the drop down lists for appropriate tools - eg the
FBAT format one will be available if you run the FBAT modelling tool.

**Attribution**
Originally designed and written for the Rgenetics
series of Galaxy tools, and
copyright Ross Lazarus 2007 (ross period lazarus at gmail period com)
Licensed under the terms of the LGPL
as documented http://www.gnu.org/licenses/lgpl.html

</help>
</tool>