given a set of genomic intervals #if $maf_source_type.maf_source == "user" #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species #else #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species #end if# --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"# --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns #end if Locally Cached Alignments Alignments in Your History Split by species Do not split Collapse empty columns Do not collapse

**What it does** This tool takes genomic coordinates, superimposes them on multiple alignments (in MAF format) stored on the Galaxy site or from your history, and excises alignment blocks corresponding to each set of coordinates. Alignment blocks that extend past START and/or END positions of an interval are trimmed. Note that a single genomic interval may correspond to two or more alignment blocks. ----- **Example** Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval: .. image:: ../static/images/maf_icons/interval2maf.png