|
6
|
1 <tool id="check_snpeff_candidates" name="CloudMap: Check snpEff Candidates">
|
|
|
2 <description>Marks up a snpEff output file with matches to a gene candidate list.</description>
|
|
|
3 <command interpreter="python">checkSnpEffCandidates.py -s $snpeff_file -c $candidate_list -o $output</command>
|
|
|
4 <inputs>
|
|
|
5 <param name="snpeff_file" type="data" format="tabular" label="SnpEff File" help="tabular output file from snpEff"/>
|
|
|
6 <param name="candidate_list" type="data" format="tabular" label="Candidate List" help="2 column list consisting of candidate genes and a description"/>
|
|
|
7 </inputs>
|
|
|
8 <outputs>
|
|
|
9 <data format="tabular" name="output" />
|
|
|
10 </outputs>
|
|
|
11 <requirements>
|
|
|
12 <requirement type="python-module">sys</requirement>
|
|
|
13 <requirement type="python-module">optparse</requirement>
|
|
|
14 <requirement type="python-module">csv</requirement>
|
|
|
15 </requirements>
|
|
|
16 <tests>
|
|
|
17 <param name="snpeff_file" value="" />
|
|
|
18 <param name="candidate_list" value="" />
|
|
|
19 </tests>
|
|
|
20 <help>
|
|
|
21
|
|
|
22 **What it does:**
|
|
|
23
|
|
|
24 Indicates on a SnpEff output file which genes are found in a candidate list by comparing Gene IDs.
|
|
|
25
|
|
|
26 For a description of the snpEff variant annotation and effect prediction tool:
|
|
|
27
|
|
|
28 http://snpeff.sourceforge.net
|
|
|
29
|
|
|
30 ------
|
|
|
31
|
|
|
32 **Input:**
|
|
|
33
|
|
|
34 The candidate list should be in a tabular format with two columns: Gene ID and Gene Description (e.g. C55B7.12 and transcription_factor). The file should contain no headers.
|
|
|
35
|
|
|
36 Useful candidate lists (e.g. transcription factors, genes expressed in neurons, transgene silencers, chromatin factors) are available on the CloudMap Galaxy page:
|
|
|
37
|
|
|
38 https://test.g2.bx.psu.edu/u/gal40/p/cloudmap
|
|
|
39
|
|
|
40
|
|
|
41 ------
|
|
|
42
|
|
|
43 **Citation:**
|
|
|
44
|
|
|
45 This tool is part of the CloudMap pipeline for analysis of mutant genome sequences. For further details, please see `Gregory Minevich, Danny Park, Richard J. Poole, Daniel Blankenberg, Anton Nekrutenko, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__
|
|
|
46
|
|
|
47 .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
|
|
|
48
|
|
|
49 Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.)
|
|
|
50 </help>
|
|
|
51 </tool>
|
