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