[2] | 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> |
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