Mercurial > repos > xuebing > sharplabtool
comparison tools/regVariation/microsatellite_birthdeath.xml @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:9071e359b9a3 |
|---|---|
| 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 | |
| 58 This 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> |