<tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1">

  <description>Alignment coverage information</description>

  <command interpreter="python">

    maf_stats.py

    #if $maf_source_type.maf_source == "user":

      $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary

    #else:

      $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary

    #end if

    ${GALAXY_DATA_INDEX_DIR}
    #if $maf_source_type.maf_source == "user":
    $input2.metadata.maf_index
    #end if

  </command>

  <inputs>

    <param format="interval" name="input1" label="Interval File" type="data">

      <validator type="unspecified_build" />

    </param>

    <conditional name="maf_source_type">

      <param name="maf_source" type="select" label="MAF Source">

        <option value="cached" selected="true">Locally Cached Alignments</option>

        <option value="user">Alignments in Your History</option>

      </param>

      <when value="user">

        <param format="maf" name="input2" label="MAF File" type="data">

          <options>

            <filter type="data_meta" ref="input1" key="dbkey" />

          </options>

          <validator type="dataset_ok_validator" />

        </param>

      </when>

      <when value="cached">

        <param name="mafType" type="select" label="MAF Type">

          <options from_file="maf_index.loc">

            <column name="name" index="0"/>

            <column name="value" index="1"/>

            <column name="dbkey" index="2"/>

            <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>

            <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>

          </options>

        </param> 

      </when>

    </conditional>

    <param name="summary" type="select" label="Type of Output">

      <option value="false" selected="true">Coverage by Region</option>

      <option value="true">Summarize Coverage</option>

    </param>

  </inputs>

  <outputs>

    <data format="interval" name="out_file1" metadata_source="input1">

      <change_format>

        <when input="summary" value="true" format="tabular" />

      </change_format>

    </data>

  </outputs>

  <requirements>

    <requirement type="python-module">numpy</requirement>

  </requirements>

  <tests>

    <test>

      <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>

      <param name="maf_source" value="cached"/>

      <param name="mafType" value="8_WAY_MULTIZ_hg17"/>

      <output name="out_file1" file="maf_stats_interval_out.dat"/>

      <param name="summary" value="false"/>

    </test>
    <test>

      <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>

      <param name="maf_source" value="cached"/>

      <param name="mafType" value="8_WAY_MULTIZ_hg17"/>

      <output name="out_file1" file="maf_stats_summary_out.dat"/>

      <param name="summary" value="true"/>

    </test>

  </tests>

  <help>



**What it does**



This tool takes a MAF file and an interval file and relates coverage information by interval for each species.

If a column does not exist in the reference genome, it is not included in the output.



Consider the interval: "chrX 1000 1100 myInterval"

  Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:



    chrX 1000 1100 myInterval H XXX YYY 

    

    chrX 1000 1100 myInterval M XXX YYY 

    

    chrX 1000 1100 myInterval R XXX YYY 

    



  where XXX and YYY are:



    XXX = number of nucleotides

    

    YYY = number of gaps



----



Alternatively, you can request only summary information for a set of intervals:

  

  ========  ===========  ========

  #species  nucleotides  coverage

  ========  ===========  ========

  hg18         30639      0.2372

  rheMac2      7524       0.0582

  panTro2      30390      0.2353

  ========  ===========  ========



  where **coverage** is the number of nucleotides divided by the total length of the provided intervals.



------



**Citation**



If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_





  </help>

</tool>