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/tools/regVariation/substitution_rates.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="subRate1" name="Estimate substitution rates " version="1.0.0">
 2  <description> for non-coding regions</description>
 3  <command interpreter="python">
 4  	substitution_rates.py 
 5  	$input 
 6  	$out_file1
 7  	#if $region.type == "win":
 8      ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol
 9    #else:
10      "None"
11    #end if 
12  </command>
13  <inputs>
14    <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
15    <conditional name="region">
16	      <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
17	         <option value="align">Alignment block</option>
18	         <option value="win">Intervals in your history</option>
19	     </param>
20	     <when value="win">
21	      	<param format="interval" name="input2" type="data" label="Choose intervals">
22	      		<validator type="unspecified_build" />
23	    	</param>
24	      </when>
25	      <when value="align" />
26      </conditional>
27  </inputs>
28  <outputs>
29    <data format="tabular" name="out_file1" metadata_source="input"/>
30  </outputs>
31  
32  <tests>
33    <test>
34      <param name="input" value="Interval2Maf_pairwise_out.maf"/>
35      <param name="type" value="align"/>
36      <output name="out_file1" file="subRates1.out"/>
37    </test>
38  </tests>
39  
40 <help> 
41
42.. class:: infomark
43
44**What it does**
45
46This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explained below:
47
48- L: number of nucleotides compared
49- N: number of different nucleotides
50- p = N/L
51
52-----
53
54.. class:: warningmark
55
56**Note**
57
58Any block/s not containing exactly two sequences, will be omitted. 
59
60  </help>  
61</tool>