/tools/regVariation/microsatellite_birthdeath.xml

 1<tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.0">
 2  <description> and causal mutational mechanisms from previously identified orthologous microsatellite sets</description>
 3  <command interpreter="perl">
 4      microsatellite_birthdeath.pl 
 5      $alignment 
 6      $orthfile 
 7      $outfile 
 8      ${alignment.metadata.species} 
 9      "$tree_definition" 
10      $thresholds
11      $separation 
12      $simthresh
13	
14  </command>
15  <inputs>
16    <page>
17        <param format="maf" name="alignment" type="data" label="Select MAF alignments"/>
18        
19        <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/>
20
21    	<param name="tree_definition" size="200" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" 
22    	help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
23      	
24      	<param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species"
25    	help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/>
26 
27     	<param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
28    	help="A value of 9,10,12,12 means: All monos having fewer than 9 repeats, dis having fewer than 5 repeats, tris having fewer than 4 repeats, tetras having fewer than 3 repeats will be excluded from the output."/>
29
30     	<param name="simthresh" size="10" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as  the above separation distance"
31    	help="Enter a value from 0 to 100"/>
32
33
34     </page>
35  </inputs>
36  <outputs>
37    <data format="txt" name="outfile" metadata_source="orthfile"/>
38  </outputs>
39  <tests>
40    <test>
41      <param name="alignment" value="chr22_5sp.maf"/>
42      <param name="orthfile" value="chr22_5sp.microraw.tabular"/>
43      <param name="thresholds" value="9,10,12,12"/>
44      <param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
45      <param name="separation" value="40"/>
46      <param name="simthresh" value="80"/>
47      <output name="outfile" file="chr22_5sp.microtab.tabular"/>
48    </test>
49  </tests>
50
51
52 <help> 
53
54.. class:: infomark
55
56**What it does**
57
58This tool uses raw orthologous microsatellite clusters (identified by the tool "Extract orthologous microsatellites") to identify microsatellite births and deaths along individual lineages of a phylogenetic tree.
59
60</help>  
61
62
63</tool>