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36 lines
1.5 KiB
XML
36 lines
1.5 KiB
XML
<tool id="maf_by_block_number1" name="Extract MAF by block number" version="1.0.1">
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<description>given a set of block numbers and a MAF file</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<command>python '$__tool_directory__/maf_by_block_number.py' '$input1' '$input2' '$out_file1' $block_col $species</command>
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<inputs>
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<param format="txt" name="input1" type="data" label="Block Numbers"/>
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<param format="maf" name="input2" label="MAF File" type="data"/>
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<param name="block_col" type="data_column" label="Column containing Block number" data_ref="input1" accept_default="True" />
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<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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<options>
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<filter type="data_meta" ref="input2" key="species" />
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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="maf_by_block_numbers.dat"/>
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<param name="input2" value="3.maf"/>
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<param name="block_col" value="1"/>
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<param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/>
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<output name="out_file1" file="maf_by_block_number_out.dat" />
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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 a list of block numbers, one per line, and extracts the corresponding MAF blocks from the provided file. Block numbers start at 0.
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</help>
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<expand macro="citations" />
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</tool>
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