Mercurial > repos > xuebing > sharplabtool
comparison tools/maf/maf_by_block_number.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 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 | |
| 30 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. | |
| 31 | |
| 32 ------ | |
| 33 | |
| 34 **Citation** | |
| 35 | |
| 36 If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ | |
| 37 | |
| 38 | |
| 39 </help> | |
| 40 </tool> |