mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
61 lines
1.8 KiB
XML
61 lines
1.8 KiB
XML
<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> |