/tools/maf/interval_maf_to_merged_fasta.xml
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1<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1"> 2 <description>given a set of genomic intervals</description> 3 <command interpreter="python"> 4 #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=${GALAXY_DATA_INDEX_DIR} 5 #else #interval_maf_to_merged_fasta.py --dbkey=$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} 6 #end if# --overwrite_with_gaps=$overwrite_with_gaps 7 </command> 8 <inputs> 9 <page> 10 <param format="interval" name="input1" type="data" label="Choose intervals"> 11 <validator type="unspecified_build" /> 12 </param> 13 <conditional name="maf_source_type"> 14 <param name="maf_source" type="select" label="MAF Source"> 15 <option value="cached" selected="true">Locally Cached Alignments</option> 16 <option value="user">Alignments in Your History</option> 17 </param> 18 <when value="user"> 19 <param name="maf_file" type="data" format="maf" label="MAF File"> 20 <options> 21 <filter type="data_meta" ref="input1" key="dbkey" /> 22 </options> 23 <validator type="dataset_ok_validator" /> 24 </param> 25 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> 26 <options> 27 <filter type="data_meta" ref="maf_file" key="species" /> 28 </options> 29 </param> 30 </when> 31 <when value="cached"> 32 <param name="maf_identifier" type="select" label="MAF Type" > 33 <options from_file="maf_index.loc"> 34 <column name="name" index="0"/> 35 <column name="value" index="1"/> 36 <column name="dbkey" index="2"/> 37 <column name="species" index="3"/> 38 <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> 39 <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/> 40 </options> 41 </param> 42 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> 43 <options from_file="maf_index.loc"> 44 <column name="uid" index="1"/> 45 <column name="value" index="3"/> 46 <column name="name" index="3"/> 47 <filter type="param_value" ref="maf_identifier" name="uid" column="1"/> 48 <filter type="multiple_splitter" column="3" separator=","/> 49 </options> 50 </param> 51 </when> 52 </conditional> 53 <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."> 54 <option value="True" selected="true">No</option> 55 <option value="False">Yes</option> 56 </param> 57 </page> 58 </inputs> 59 <outputs> 60 <data format="fasta" name="out_file1" /> 61 </outputs> 62 <tests> 63 <test> 64 <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/> 65 <param name="maf_source" value="cached"/> 66 <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/> 67 <param name="species" value="hg18,mm8"/> 68 <param name="overwrite_with_gaps" value="True"/> 69 <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" /> 70 </test> 71 <test> 72 <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> 73 <param name="maf_source" value="cached"/> 74 <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> 75 <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> 76 <param name="overwrite_with_gaps" value="True"/> 77 <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" /> 78 </test> 79 <test> 80 <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> 81 <param name="maf_source" value="user"/> 82 <param name="maf_file" value="5.maf"/> 83 <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> 84 <param name="overwrite_with_gaps" value="True"/> 85 <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" /> 86 </test> 87 </tests> 88 <help> 89**What it does** 90 91A 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: 92 93 * finds all MAF blocks that overlap the interval; 94 * sorts MAF blocks by alignment score; 95 * stitches blocks together and resolves overlaps based on alignment score; 96 * outputs alignments in FASTA format. 97 98------ 99 100**Example** 101 102Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps: 103 104.. image:: ../static/images/maf_icons/stitchMaf.png 105 106 </help> 107</tool>