Mercurial > repos > devteam > microsatellite_birthdeath
changeset 1:a9d119f2cace draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:25:46 -0400 |
| parents | 6611321d8bbb |
| children | |
| files | microsatellite_birthdeath.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/microsatellite_birthdeath.xml Tue Aug 20 11:01:05 2013 -0400 +++ b/microsatellite_birthdeath.xml Tue Oct 13 12:25:46 2015 -0400 @@ -24,16 +24,16 @@ </options> </param> - <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" + <param name="tree_definition" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/> - <param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species" + <param name="separation" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species" help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/> - <param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites" + <param name="thresholds" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites" 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."/> - <param name="simthresh" size="10" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as the above separation distance" + <param name="simthresh" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as the above separation distance" help="Enter a value from 0 to 100"/> @@ -63,6 +63,7 @@ **What it does** 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. + ----- .. class:: warningmark