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comparison microsatellite_birthdeath.xml @ 1:a9d119f2cace draft default tip

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:25:46 -0400
parents 6611321d8bbb
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0:6611321d8bbb 1:a9d119f2cace
22 <options> 22 <options>
23 <filter type="data_meta" ref="alignment" key="species" /> 23 <filter type="data_meta" ref="alignment" key="species" />
24 </options> 24 </options>
25 </param> 25 </param>
26 26
27 <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" 27 <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"
28 help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/> 28 help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
29 29
30 <param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species" 30 <param name="separation" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species"
31 help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/> 31 help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/>
32 32
33 <param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites" 33 <param name="thresholds" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
34 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."/> 34 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."/>
35 35
36 <param name="simthresh" size="10" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as the above separation distance" 36 <param name="simthresh" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as the above separation distance"
37 help="Enter a value from 0 to 100"/> 37 help="Enter a value from 0 to 100"/>
38 38
39 39
40 </page> 40 </page>
41 </inputs> 41 </inputs>
61 .. class:: infomark 61 .. class:: infomark
62 62
63 **What it does** 63 **What it does**
64 64
65 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. 65 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.
66
66 ----- 67 -----
67 68
68 .. class:: warningmark 69 .. class:: warningmark
69 70
70 **Note** 71 **Note**