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1 <tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.0">
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2 <description> and causal mutational mechanisms from previously identified orthologous microsatellite sets</description>
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3 <command interpreter="perl">
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4 microsatellite_birthdeath.pl
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5 $alignment
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6 $orthfile
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7 $outfile
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8 ${alignment.metadata.species}
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9 "$tree_definition"
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10 $thresholds
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11 $separation
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12 $simthresh
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13
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14 </command>
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15 <inputs>
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16 <page>
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17 <param format="maf" name="alignment" type="data" label="Select MAF alignments"/>
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18
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19 <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/>
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20
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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"
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22 help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
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23
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24 <param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species"
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25 help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/>
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26
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27 <param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
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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."/>
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29
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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"
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31 help="Enter a value from 0 to 100"/>
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32
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33
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34 </page>
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35 </inputs>
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36 <outputs>
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37 <data format="txt" name="outfile" metadata_source="orthfile"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="alignment" value="chr22_5sp.maf"/>
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42 <param name="orthfile" value="chr22_5sp.microraw.tabular"/>
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43 <param name="thresholds" value="9,10,12,12"/>
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44 <param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
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45 <param name="separation" value="40"/>
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46 <param name="simthresh" value="80"/>
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47 <output name="outfile" file="chr22_5sp.microtab.tabular"/>
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48 </test>
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49 </tests>
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50
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51
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52 <help>
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53
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54 .. class:: infomark
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55
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56 **What it does**
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57
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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.
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59
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60 </help>
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61
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62
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63 </tool>
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