<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1">

  <description>given a set of genomic intervals</description>

  <command interpreter="python">

    #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}

    #else                                     #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}

    #end if# --overwrite_with_gaps=$overwrite_with_gaps

  </command>

  <inputs>

    <page>

        <param format="interval" name="input1" type="data" label="Choose intervals">

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

                <options>

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

                </options>

                <validator type="dataset_ok_validator" />

              </param>

              <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">

                <options>

                  <filter type="data_meta" ref="maf_file" key="species" />

                </options>

              </param>

            </when>

            <when value="cached">

              <param name="maf_identifier" 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"/>

                  <column name="species" index="3"/>

                  <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> 

              <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">

                <options from_file="maf_index.loc">

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

                  <column name="value" index="3"/>

                  <column name="name" index="3"/>

                  <filter type="param_value" ref="maf_identifier" name="uid" column="1"/>

                  <filter type="multiple_splitter" column="3" separator=","/>

                </options>

              </param>

            </when>

        </conditional>

        <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block.">

          <option value="True" selected="true">No</option>

          <option value="False">Yes</option>

        </param>

    </page>

   </inputs>

  <outputs>

    <data format="fasta" name="out_file1" />

  </outputs>

  <tests>

    <test>

      <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/>

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

      <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/>

      <param name="species" value="hg18,mm8"/>

      <param name="overwrite_with_gaps" value="True"/>

      <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" />

    </test>

    <test>

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

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

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

      <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>

      <param name="overwrite_with_gaps" value="True"/>

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

    </test>

    <test>

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

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

      <param name="maf_file" value="5.maf"/>

      <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>

      <param name="overwrite_with_gaps" value="True"/>

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

    </test>

  </tests>

  <help>

**What it does**



A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of genomic intervals. For every interval it performs the following:



  * finds all MAF blocks that overlap the interval;

  * sorts MAF blocks by alignment score;

  * stitches blocks together and resolves overlaps based on alignment score;

  * outputs alignments in FASTA format.



------



**Example**



Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps:



.. image:: ../static/images/maf_icons/stitchMaf.png



  </help>

</tool>