/tools/maf/maf_by_block_number.xml
XML | 32 lines | 30 code | 2 blank | 0 comment | 0 complexity | 556003ccd252a8813a27f116442bebc8 MD5 | raw file
1<tool id="maf_by_block_number1" name="Extract MAF by block number" version="1.0.1"> 2 <description>given a set of block numbers and a MAF file</description> 3 <command interpreter="python">maf_by_block_number.py $input1 $input2 $out_file1 $block_col $species</command> 4 <inputs> 5 <param format="txt" name="input1" type="data" label="Block Numbers"/> 6 <param format="maf" name="input2" label="MAF File" type="data"/> 7 <param name="block_col" type="data_column" label="Column containing Block number" data_ref="input1" accept_default="True" /> 8 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> 9 <options> 10 <filter type="data_meta" ref="input2" key="species" /> 11 </options> 12 </param> 13 </inputs> 14 <outputs> 15 <data format="maf" name="out_file1" /> 16 </outputs> 17 <tests> 18 <test> 19 <param name="input1" value="maf_by_block_numbers.dat"/> 20 <param name="input2" value="3.maf"/> 21 <param name="block_col" value="1"/> 22 <param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/> 23 <output name="out_file1" file="maf_by_block_number_out.dat" /> 24 </test> 25 </tests> 26 <help> 27 28**What it does** 29 30This 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. 31 </help> 32</tool>