/tools/regVariation/substitution_rates.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 61 lines · 50 code · 11 blank · 0 comment · 0 complexity · 199b18379b2600b9b894ca82e48cecbe MD5 · raw file
- <tool id="subRate1" name="Estimate substitution rates " version="1.0.0">
- <description> for non-coding regions</description>
- <command interpreter="python">
- substitution_rates.py
- $input
- $out_file1
- #if $region.type == "win":
- ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol
- #else:
- "None"
- #end if
- </command>
- <inputs>
- <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
- <conditional name="region">
- <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
- <option value="align">Alignment block</option>
- <option value="win">Intervals in your history</option>
- </param>
- <when value="win">
- <param format="interval" name="input2" type="data" label="Choose intervals">
- <validator type="unspecified_build" />
- </param>
- </when>
- <when value="align" />
- </conditional>
- </inputs>
- <outputs>
- <data format="tabular" name="out_file1" metadata_source="input"/>
- </outputs>
-
- <tests>
- <test>
- <param name="input" value="Interval2Maf_pairwise_out.maf"/>
- <param name="type" value="align"/>
- <output name="out_file1" file="subRates1.out"/>
- </test>
- </tests>
-
- <help>
- .. class:: infomark
- **What it does**
- 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:
- - L: number of nucleotides compared
- - N: number of different nucleotides
- - p = N/L
- -----
- .. class:: warningmark
- **Note**
- Any block/s not containing exactly two sequences, will be omitted.
- </help>
- </tool>