/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml

 1<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1">
 2  <description> for multiple (>2) species alignments</description>
 3  <command interpreter="perl">
 4    multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl   	
 5    $input1 
 6  	$out_file1 
 7  	$thresholds 
 8  	$species 
 9  	"$treedefinition"
10  	$separation 
11	
12  </command>
13  <inputs>
14    <page>
15        <param format="maf" name="input1" type="data" label="Select MAF alignments"/>
16       	<param name="separation" size="10" type="integer" value="10" label="Minimum base pair distance between adjacent microsatellite blocks"
17    	help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/>
18    	<param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
19    	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."/>
20        <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1">
21      	<options>
22        	<filter type="data_meta" ref="input1" key="species" />
23      	</options>
24    	</param>
25    	<param name="treedefinition" size="200" type="text" value = "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" 
26    	help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
27    </page>
28  </inputs>
29  <outputs>
30    <data format="txt" name="out_file1" metadata_source="input1"/>
31  </outputs>
32  <requirements>
33     <requirement type="binary">sputnik</requirement>
34  </requirements>
35  <tests>
36    <test>
37      <param name="input1" value="chr22_5sp.maf"/>
38      <param name="thresholds" value="9,10,12,12"/>
39      <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/>
40      <param name="treedefinition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
41      <param name="separation" value="10"/>
42      <output name="out_file1" file="chr22_5sp.microraw.tabular"/>
43    </test>
44  </tests>
45
46 <help> 
47
48.. class:: infomark
49
50**What it does**
51
52This tool finds ortholgous microsatellite blocks between aligned species
53  
54</help>  
55
56
57</tool>