Mercurial > repos > devteam > microsatellite_birthdeath
annotate microsatellite_birthdeath.xml @ 2:da3e903b8c3e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:21:05 -0500 |
| parents | d1f31a7d7c65 |
| children |
| rev | line source |
|---|---|
| 0 | 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 $species | |
| 9 "$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 that have NOT been masked for nucleotide quality"/> | |
| 18 | |
| 19 <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/> | |
| 20 | |
| 21 <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"> | |
| 22 <options> | |
| 23 <filter type="data_meta" ref="alignment" key="species" /> | |
| 24 </options> | |
| 25 </param> | |
| 26 | |
|
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da3e903b8c3e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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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" |
| 0 | 28 help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/> |
| 29 | |
|
2
da3e903b8c3e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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30 <param name="separation" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species" |
| 0 | 31 help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/> |
| 32 | |
|
2
da3e903b8c3e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
33 <param name="thresholds" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites" |
| 0 | 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 | |
|
2
da3e903b8c3e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
36 <param name="simthresh" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as the above separation distance" |
| 0 | 37 help="Enter a value from 0 to 100"/> |
| 38 | |
| 39 | |
| 40 </page> | |
| 41 </inputs> | |
| 42 <outputs> | |
| 43 <data format="txt" name="outfile" metadata_source="orthfile"/> | |
| 44 </outputs> | |
| 45 <tests> | |
| 46 <test> | |
| 47 <param name="alignment" value="regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz"/> | |
| 48 <param name="orthfile" value="regVariation/microsatellite/Galaxy17_short_raw.txt"/> | |
| 49 <param name="thresholds" value="9,10,12,12"/> | |
| 50 <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/> | |
| 51 <param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/> | |
| 52 <param name="separation" value="10"/> | |
| 53 <param name="simthresh" value="85"/> | |
| 54 <output name="outfile" file="regVariation/microsatellite/Galaxy17_unmasked_results.txt"/> | |
| 55 </test> | |
| 56 </tests> | |
| 57 | |
| 58 | |
| 59 <help> | |
| 60 | |
| 61 .. class:: infomark | |
| 62 | |
| 63 **What it does** | |
| 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. | |
|
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d1f31a7d7c65
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947
devteam
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diff
changeset
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66 |
| 0 | 67 ----- |
| 68 | |
| 69 .. class:: warningmark | |
| 70 | |
| 71 **Note** | |
| 72 | |
| 73 A tab-separated output table (depending on the species being considered) is generated where each row contains all information for a microsatellite locus from multiple species. | |
| 74 The table typically reads like this: | |
| 75 | |
| 76 hg18.chr22 16153057 16153074 A 1 ins=,imot:0:tt;dels= ,9:t>c -panTro2 hg18:tttttttttttttttttt,ponAbe2:--tttttttttttttttt,panTro2:-----ttttctttttttt | |
| 77 | |
| 78 hg18.chr22 16131711 16131722 ATGC 4 NA ,2:C>T +ponAbe2 hg18:CACGCATGCATG,ponAbe2:CATGCATGCATG,panTro2:CACGCATGCATG,rheMac2:CACGCGTGCATG | |
| 79 | |
| 80 Where columns list the following: | |
| 81 | |
| 82 1: Chromosome/scaffold/contig of one of the species. The species chosen is the first species readable in the Newick tree submitted by the user. | |
| 83 | |
| 84 2: Start coordinate | |
| 85 | |
| 86 3: End coordinate | |
| 87 | |
| 88 4: Motif of microsatellite | |
| 89 | |
| 90 5: Motif size | |
| 91 | |
| 92 6: Insertion and deletion details. Insertions are separated from deletions by a ";", and individual insertions and deletions are separated from others by a comma. For the purpose of illustration, consider the first row listed above: | |
| 93 "imot:0:tt", where imot/imotf again suggest insertion, the number indicates position of insertion within the microsatellite's alignment, and this is followed by identity of nucleotides that are inserted. | |
| 94 | |
| 95 7: Substitution details. Individual substitutions are separated by commas. Each entry contains the position of substitution event in the microsatellites' alignment, and the nature of substitution. | |
| 96 | |
| 97 8: Inference of birth/death event. Births are indicated by "+", and deaths by "-". Events such as "-hg18:panTro2" suggest death in the common ancestor of hg18 and panTro2, whereas events such as "-hg18.panTro2" indicate parallel, independent death events along the two lineages. Alternative interpretations of the event may also be listed, following a "/", such as: | |
| 98 "+hg18.+panTro2 / +hg18:panTro2" | |
| 99 | |
| 100 9: Actual sequences in the alignment, separated by commas. | |
| 101 | |
| 102 </help> | |
| 103 | |
| 104 | |
| 105 </tool> |