comparison checkSnpEffCandidates.xml @ 6:22c8c4f8d11c draft

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author gregory-minevich
date Mon, 25 Jun 2012 16:13:18 -0400
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5:c7b8f28dfc93 6:22c8c4f8d11c
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>