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1 <tool id="check_snpeff_candidates" name="CloudMap: Check snpEff Candidates">
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2 <description>Marks up a snpEff output file with matches to a gene candidate list.</description>
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3 <command interpreter="python">checkSnpEffCandidates.py -s "$snpeff_file" -c "$candidate_list" -o "$output"</command>
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4 <inputs>
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5 <param name="snpeff_file" type="data" format="tabular" label="SnpEff File" help="tabular output file from snpEff"/>
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6 <param name="candidate_list" type="data" format="tabular" label="Candidate List" help="2 column list consisting of candidate genes and a description"/>
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7 </inputs>
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8 <outputs>
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9 <data format="tabular" name="output" />
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10 </outputs>
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11 <requirements>
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12 <requirement type="python-module">sys</requirement>
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13 <requirement type="python-module">optparse</requirement>
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14 <requirement type="python-module">csv</requirement>
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15 </requirements>
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16 <tests>
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17 <param name="snpeff_file" value="" />
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18 <param name="candidate_list" value="" />
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19 </tests>
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20 <help>
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21
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22 **What it does:**
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23
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24 Indicates on a SnpEff output file which genes are found in a candidate list by comparing Gene IDs.
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25
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26 For a description of the snpEff variant annotation and effect prediction tool:
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27
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28 http://snpeff.sourceforge.net
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29
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30 ------
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31
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32 **Input:**
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33
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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.
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35
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36 Useful candidate lists (e.g. transcription factors, genes expressed in neurons, transgene silencers, chromatin factors) are available on the CloudMap Galaxy page:
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37
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38 http://usegalaxy.org/cloudmap
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39
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40
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41 ------
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42
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43 **Citation:**
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44
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45 This tool is part of the CloudMap pipeline for analysis of mutant genome sequences. For further details, please see `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__
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46
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47 .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
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48
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49 Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.)
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50 </help>
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51 </tool>
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