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1 <tool id="subRate1" name="Estimate substitution rates " version="1.0.0">
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2 <description> for non-coding regions</description>
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3 <command interpreter="python">
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4 substitution_rates.py
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5 $input
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6 $out_file1
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7 #if $region.type == "win":
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8 ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol
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9 #else:
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10 "None"
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11 #end if
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12 </command>
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13 <inputs>
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14 <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
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15 <conditional name="region">
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16 <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
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17 <option value="align">Alignment block</option>
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18 <option value="win">Intervals in your history</option>
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19 </param>
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20 <when value="win">
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21 <param format="interval" name="input2" type="data" label="Choose intervals">
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22 <validator type="unspecified_build" />
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23 </param>
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24 </when>
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25 <when value="align" />
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26 </conditional>
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27 </inputs>
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28 <outputs>
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29 <data format="tabular" name="out_file1" metadata_source="input"/>
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30 </outputs>
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31
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32 <tests>
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33 <test>
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34 <param name="input" value="Interval2Maf_pairwise_out.maf"/>
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35 <param name="type" value="align"/>
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36 <output name="out_file1" file="subRates1.out"/>
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37 </test>
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38 </tests>
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39
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40 <help>
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41
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42 .. class:: infomark
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43
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44 **What it does**
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45
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46 This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explained below:
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47
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48 - L: number of nucleotides compared
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49 - N: number of different nucleotides
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50 - p = N/L
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51
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52 -----
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53
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54 .. class:: warningmark
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55
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56 **Note**
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57
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58 Any block/s not containing exactly two sequences, will be omitted.
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59
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60 </help>
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61 </tool> |
