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/tools/maf/maf_by_block_number.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 40 lines | 33 code | 7 blank | 0 comment | 0 complexity | 2bdda4d69b25e6c9443539f1546005f3 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
32------
33
34**Citation**
35
36If 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
37
38
39  </help>
40</tool>