<tool id="rgQC1" name="QC reports:">

    <description>Marker and Subject measures</description>

    <command interpreter="python">
        rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$title"
        -s '$html_file' -p '$html_file.files_path'
    </command>

    <inputs>
          <param name="input_file" type="data" label="RGenetics genotype file in compressed Plink format"
          size="80" format="pbed" />
       <param name="title" size="80" type="text" value="RgQC report" label="Descriptive report title"/>
   </inputs>

   <outputs>
       <data format="html" name="html_file" metadata_source="input_file" label="${title}.html"/>
   </outputs>

<tests>
 <test>
    <param name='input_file' value='tinywga' ftype='pbed' >
    <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='rgQCtest1' />
    <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='300'>
    <param name="dbkey" value="hg18" />
    <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "100000"/>
    <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/>
    <extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" />
    <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/>
    <extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" lines_diff="90"/>
    <extra_files type="file" name='tinywga.imendel' value="rgtestouts/rgQC/tinywga.imendel" compare="diff"/>
    <extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" />
    <extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" />
    <extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" />
    <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="sim_size" delta="100000"/>
    <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" lines_diff="10" />
    <extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="sim_size" delta="1000" />
    <extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" />
    <extra_files type="file" name='ldp_tinywga.log' value="rgtestouts/rgQC/ldp_tinywga.log" compare="diff" lines_diff="20"/>
    <extra_files type="file" name='Ranked_Marker_HWE.xls' value="rgtestouts/rgQC/Ranked_Marker_HWE.xls" compare="diff" />
    <extra_files type="file" name='Ranked_Marker_MAF.xls' value="rgtestouts/rgQC/Ranked_Marker_MAF.xls" compare="diff" />
    <extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" lines_diff="5"/>
    <extra_files type="file" name='Ranked_Subject_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls" compare="diff" lines_diff="40"/>
    <extra_files type="file" name='tinywga_fracmiss_cum.jpg' value="rgtestouts/rgQC/tinywga_fracmiss_cum.jpg" compare="sim_size" delta = "20000"/>     
    <extra_files type="file" name='tinywga_fracmiss_cum.pdf' value="rgtestouts/rgQC/tinywga_fracmiss_cum.pdf" compare="sim_size" delta = "100000"/>     
 </output>
 </test>
</tests>
 <help>

.. class:: infomark

**Summary**

This tool prepares an extensive and comprehensive series of reports for quality control checking of SNP genotypes from any arbitrary
genotyping experiment. Designed for family based data, so includes optional reports on Mendelian errors by
subject and by marker.

The outputs include histograms and boxplots for missingness, maf, mendel counts and hwe by marker, and the ones that make sense by
subject. The report is built as a single web page containing links to the summary marker and subject files.

The F (inbreeding) statistic is calculated using a somewhat LD independent group of genotypes
The Plink used is --indep-pairwise 40 20 0.5 until we make it configurable.
High heterozygosity might mean contaminated sample - more than one DNA. Low heterozygosity might mean inbreeding as in strains
of mice.

If the data file you want is missing from the option list above,
you will first need to "import" it so it will be available here. Files available in the system library
can be imported by selecting and completing the "Import ped/map" choice from the Get Data tool group at the top of the Galaxy
menu. Your system administrator will be responsible for adding files to the system library.

-----

.. class:: infomark

**Syntax**

- **Genotype file** is the input pedfile -
- **Prefix** is a string used to name all of the outputs

-----

**Attribution**

This Galaxy tool was written by Ross Lazarus for the Rgenetics project
The current version uses Plink for most calculations and R for plotting - for full Plink attribution, source code and documentation,
please see http://pngu.mgh.harvard.edu/~purcell/plink/ while R attribution and source code can be found at http://r-project.org

Shaun Purcell provides the documentation you need specific to those settings, at
http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#glm

Tool and Galaxy datatypes originally designed and written for the Rgenetics
series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus@gmail.com)
Shaun Purcell created and maintains Plink, while a cast of many maintain R.

Please acknowledge your use of this tool, Galaxy, R and Plink in your publications and let
us know so we can keep track. These tools all rely on highly competitive grant funding
so your letting us know about publications is important to our ongoing support.

</help>



</tool>