given a set of genomic intervals macros.xml python '$__tool_directory__/interval_maf_to_merged_fasta.py' --dbkey='$dbkey' --species='$maf_source_type.species' #if $maf_source_type.maf_source == "user" --mafSource='$maf_source_type.maf_file' --mafIndex='$maf_source_type.maf_file.metadata.maf_index' #else --mafSource='$maf_source_type.maf_identifier' #end if --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}' --overwrite_with_gaps='$overwrite_with_gaps' Locally Cached Alignments Alignments in Your History No Yes

**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_path}/images/maf_icons/stitchMaf.png