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40 lines
1.8 KiB
XML
40 lines
1.8 KiB
XML
<tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks">
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<description>given a set of genomic intervals</description>
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<command interpreter="python2.4">interval2maf_pairwise.py --dbkey=$dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$mafType --interval_file=$input1 --output_file=$out_file1</command>
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<inputs>
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<param name="input1" type="data" format="interval" label="Interval File"/>
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<param name="mafType" type="select" label="Choose MAF source">
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<options from_file="/depot/data2/galaxy/maf_pairwise.loc">
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<filter type="data_meta" data_ref="input1" key="build" />
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<filter type="column" name="build_col" value="2" />
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<filter type="column" name="name_col" value="0" />
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<filter type="column" name="value_col" value="1" />
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</options>
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</param>
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</inputs>
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<outputs>
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<data format="maf" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="8.bed" dbkey="hg17" format="bed"/>
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<param name="mafType" value="PAIRWISE_hg17_fr1"/>
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<output name="out_file1" file="Interval2Maf_pairwise_out.maf"/>
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</test>
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</tests>
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<help>
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**What it does**
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This tool takes genomic coordinates, superimposes them on pairwise alignments (in MAF format) stored on the Galaxy site, 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.
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-----
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**Example**
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Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval:
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.. image:: ../static/images/maf_icons/interval2maf.png
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</help>
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</tool>
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