<tool id="lookup5" name="Lookup table" version="5.0.0">
	<description> for 2cM intervals</description>
	<command interpreter="python">
            lookup.py --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1 --output2 $output2
	</command>
        <inputs>
            <param label="Markers file" name="input1" type="data" format="tabular" help="Tabular file giving marker positions in cM and bp"></param>
            <param label="QTL Cartographer Z file" name="input2" type="data" format="tabular" help="QTL Cartographer output file (.z)"></param>
	    <param label="Chromosome length file" name="input3" type="data" format="tabular" help="A tabular file giving the length of each chromosome in bp"></param>
        </inputs>
	<outputs>
                <data format="tabular" name="output1" />
		<data format="tabular" name="output2" />
	</outputs>
	<requirements>
	</requirements>
	<tests>
          <test>
          </test>
	</tests>
	<help>
		
**What it does**

The information from the Markers file and the QTL Cartographer Z file, are combined to proportionally estimate a base pair position at each “QTL Cartographer bin” (e.g. 2 cM intervals).

The Lookup file can then serve as a lookup table to convert between base pair and centimorgan positions.

-------

**Example input files**

Markers file, each row correspond to a marker (5 columns; only a part of the file is shown)::

 chr	marker	name	cM	bp
 1	1	marker1	0	2038278
 1	2	marker2	7.53	3649871
 1	3	marker3	18.77	6155281
 1	4	marker4	38.71	12398322
 1	5	marker5	44.62	14171692
 1	6	marker6	48.73	16529505

QTL Cartographer Z file, each row correspond to a 2cM interval (the example shows part of the important part of the Z file, the first 3 data columns of the first block). Note: Headers is fine and will be ignored::

 1	1	0.0001	…
 1	1	0.0201	…
 1	1	0.0401	…
 1	1	0.0601	…
 1	2	0.0754	…
 1	2	0.0954	…
 1	2	0.1154	…
 1	2	0.1354	…
 1	2	0.1554	…
 1	2	0.1754	…
 1	3	0.1878	…
 1	3	0.2078	…
 1	3	0.2278	…
 1	3	0.2478	… 

Chromosome length file, each row correspond to a chromosome (2 columns; only a part of the file is shown)::

 chr1	301354135
 chr2	237068873
 chr3	232140174
 chr4	241473504
 chr5	217872852
 chr6	169174353

-------

**Example output files**


Lookup output file, each row correspond to a 2 cM interval (7 columns; only a part of the file is shown)::

 int.id	chr	marker	int	cM	bp	length_cM
 1	1	1	0.0001	0.0	2038278	2.0
 2	1	1	0.0201	2.0	2466324	2.0
 3	1	1	0.0401	4.0	2894370	2.0
 4	1	1	0.0601	6.0	3322416	1.53
 5	1	2	0.0754	7.53	3649871	2.0
 6	1	2	0.0954	9.53	4095673	2.0
 7	1	2	0.1154	11.53	4541476	2.0
 8	1	2	0.1354	13.53	4987278	2.0

Chromosome summary file, each row correspond to a chromosome (6 columns; only a part of the file is shown). The last row gives the total across the genome::

 chr	markers	cM	bp	int_positions	bins
 1	27	324.4	301354135	177	176
 2	14	169.11	237068873	92	91
 3	19	221.29	232140174	123	122
 4	20	188.37	241473504	105	104
 5	20	203.82	217872852	110	109
 6	17	195.85	169174353	106	105
 Total 	117	1302.84	1399083891	713	707

        </help>
</tool>