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pySInBaD.xml
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<tool id="sinbad" name="SInBaD" version="0.1">
<requirements>
<requirement type="package" version=""></requirement>
</requirements>
<description>Exploring functional variant discovery in non-coding regions
</description>
<command interpreter="python">
pySInBaD.py $input $infile.ftype $fdr > $output
</command>
<inputs>
<page>
<conditional name="infile">
<param name="ftype" type="select" label="File Type" help="TODO: add support for more file formats!">
<option value="csv" selected="True">CSV format</option>
<option value="vcf">VCF format</option>
<option value="txt">Text format</option>
</param>
<when value="csv">
<param format="csv" name="input" type="data" label="Query File in CSV" help="data in 1 - based coordinate system."/>
</when>
<when value="vcf">
<param format="vcf" name="input" type="data" label="Query File in VCF" help="data in 1 - based coordinate system."/>
</when>
<when value="txt">
<param format="txt" name="input" type="data" label="Query File in TXT" help="data in 1 - based coordinate system."/>
</when>
</conditional>
<param name="outname" label="Name for output file to make it easy to remember what you did" type="text" size="50" value="SInBaD_run" />
<!-- future multiple genome db handler -->
<param name="org_name" type="select" label="Organism" help="TODO: add more genomes!">
<option value="h_sapiens" selected="True">Homo sapiens (hg19)</option>
</param>
<param name="fdr" type="select" label="False Discovery Rate" help="Please see below for details.">
<option value="-1" selected="True">-1</option>
<option value="0">0</option>
<option value="1">1</option>
<option value="5">5</option>
</param>
<param name="outform" type="select" label="Output Format" help="TODO: add support for more result file formats!">
<option value="csv" selected="True">CSV output format</option>
<option value="txt">Text output format</option>
</param>
</page>
</inputs>
<outputs>
<data format="csv" name="output" label="${outname}_output.${outform}" >
<change_format>
<when input="outform" value="txt" format="txt" />
</change_format>
</data>
</outputs>
<!-- TODO add functional test for the tool -->
<tests>
<test>
</test>
</tests>
<help>
**Note**
Exploring functional variant discovery in non-coding regions with SInBaD (Sequence-Information-Based-Decision-model).
**What it does**
Based on the nucleotide conservation information `SInBaD`_ evaluate any annotated human nucleotide variant in all known exons, introns, splice junctions and promoter regions.
.. _SInBaD: http://nar.oxfordjournals.org/content/early/2012/08/30/nar.gks800
------
**Example**
- The following genomic location, reference and alternate allele data of human in CSV format::
#Chromosome, Position(hg19-ucsc), Original Basepair, Mutation
chr1,12190,C,A
chr1,12191
chr1,12192,A,T
- will give result in CSV format as follows::
#Chromosome, Position(hg19-ucsc), Original Basepair, Mutation, Score, Region
chr1,12190,C,A,0.0878524532997843,c
chr1,12191,A,A,0.10677613930990437,c
chr1,12191,T,G,0.23030976815074622,c
chr1,12192,A,T,0.10677613930990437,c
------
**False Discovery Rate**
+-------------+------------+------------+-----------+
|FDR threshold|Coding |Intron |Promoter |
+=============+============+============+===========+
|Default |0 |0 |0 |
+-------------+------------+------------+-----------+
|Default |0.5 |0.5 |0.5 |
+-------------+------------+------------+-----------+
|1% FPR |0.8569335937|0.8359375 |0.879031186|
+-------------+------------+------------+-----------+
|5% FPR |0.732421875 |0.458984375 |0.784355163|
+-------------+------------+------------+-----------+
------
**Licenses**
If **SInBaD** is used to obtain results for scientific publications it
should be cited as [1]_.
.. [1] Kjong-Van Lehmann and Ting Chen. `Exploring functional variant discovery in non-coding regions with SInBaD`_. Nucl. Acids Res. (2012)
.. _Exploring functional variant discovery in non-coding regions with SInBaD: http://nar.oxfordjournals.org/content/early/2012/08/30/nar.gks800
------
**Attribution**
The first iteration of this Galaxy wrapper was written by vipin at cbio.mskcc.org
This wrapper is released licensed under the LGPL_
.. _LGPL: http://www.gnu.org/copyleft/lesser.html
</help>
</tool>