<tool id="rgPedSub1" name="Subset markers:">

    <description>region or rs list</description>

    <command interpreter="python">
        rgPedSub.py $script_file
    </command>

    <inputs>
        <page>
       <param name="title" type="text" size="80" label="Title for output files"
        help="Descriptive title for new genotype/map files" value="Genotype_Subset" />
       <param name="input1" type="data" format="lped"
   		label="Current history lPed format data" optional="false"
    	size="120" help="Choose a Linkage Ped format data from your current history" />
       <param name='relfilter' label = "Filter out family relatedness" type="select"
   	     optional="false" size="132"
         help="Optionally remove related subjects if pedigree identifies founders and their offspring">
         <option value="all" selected='true'>No filter on relatedness - all subjects passed through</option>
         <option value="fo" >Founders only (pedigree mother and father ID = "0")</option>
         <option value="oo" >Offspring only (one randomly chosen if >1 sibs in family)</option>
   		</param>

        </page><page>
       <conditional name="m">
	        <param name="mtype" type="select"  label="Markers in a genomic interval,or as an rs list?" refresh_on_change='true'
	        help="Indicate the markers to be saved - as a list or as genomic region coordinates">
	          <option value="grslist" >Cut and paste a list of marker ids as rs numbers</option>
	          <option value="gregion" selected='true'>Supply genomic coordinates for a region (as UCSC location)</option>
	        </param>
	        <when value="gregion">
	         <param name="region" type="text" label="Genomic refseq coordinates - chromosome:start-end"
        		size="120" help="Region to be saved as chr9:119,506,000-119,518,000"/>
	       	  <param name="rslist" type="hidden" value='' />
	        </when>
	        <when value="grslist">
	          <param name="region" value="" type="hidden"/>
	       	    <param name="rslist" type="text" area='true' size='15x20' label="marker id (rs) list"
       			help="Cut and paste, or type a list of marker ids separated by spaces"  />
	        </when>
        </conditional>
        </page>
   </inputs>

   <outputs>
       <data format="lped" name="output1" metadata_source="input1" label="${title}.lped"/>
   </outputs>

<configfiles>
<configfile name="script_file">
title~~~~$title
output1~~~~$output1
userId~~~~$userId
outformat~~~~lped
basename~~~~$input1.metadata.base_name
inped~~~~$input1.extra_files_path/$input1.metadata.base_name
outdir~~~~$output1.files_path
relfilter~~~~$relfilter
#if $m.mtype=='grslist'
rslist~~~~$m.rslist
region~~~~
#else
rslist~~~~
region~~~~$m.region
#end if
</configfile>
</configfiles>

<tests>
 <test>
    <param name='input1' value='tinywga' ftype='lped' >
    <metadata name='base_name' value='tinywga' />
    <composite_data value='tinywga.ped' />
    <composite_data value='tinywga.map' />
    <edit_attributes type='name' value='tinywga' /> 
    </param>
    <param name='title' value='rgPedSubtest1' />
    <param name="mtype" value="grslist" />
    <param name="region" value="" />
    <param name="rslist" value="rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" />
    <param name="relfilter" value="all" />
    <output name='output1' file='rgtestouts/rgPedSub/rgPedSubtest1.lped' ftype='lped' linesDiff='7'/>
 </test>
</tests>

<help>

.. class:: infomark

**Note**

There are 2 forms to complete before the job is ready to be run

  **Page 1**

     give the job a mnemonic descriptive title and select the output format.

     Choose a file containing genotypes and a pedigree from your current history

     The input file must be in linkage ped format.

     If the data are not yet in your history, import from one of the system libraries or upload from your computer using the get data tool

  **Page 2**

     Define the markers to be used. You can supply a UCSC style location as chr:start_offset-end_offset

     or a list of marker ids - rs numbers. You can flip between marker input style by changing the select box.

     If you supply a list, the markers must all be from the same chromosome or region for sensible results.

Run the job and the subset file will eventually appear in your history ready to be used with other tools.

-----

**Syntax**

- **Library Linkage Ped** is a linkage format pedigree file chosen from the system file Library
- **History Linkage Ped** is a linkage format pedigree file chosen from your current Galaxy History
- **Region** is the genomic region cut and paste from a UCSC browser location window
- **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data

-----

.. class:: infomark

**Summary**

This tool is a special purpose tool to extract genotypes from genotype data in linkage
pedigree format (separate map file) over a specified genomic region
The region to be extracted can be described as UCSC browser location, or as a list of
markers.

It is possible to retain ALL markers by leaving the rslist and region empty if you just want to remove
all offspring from a pedigree for example

The extracted data will appear in your current history as a new lped data set

Copyright, Ross Lazarus, March 2008 for the Rgenetics project
Released under the LGPL. See http://www.gnu.org/licenses/lgpl.html for license terms.

</help>
</tool>