Mercurial > repos > xuebing > sharplabtool
comparison tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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 | |
52 This tool finds ortholgous microsatellite blocks between aligned species | |
53 | |
54 </help> | |
55 | |
56 | |
57 </tool> |