Mercurial > repos > jjohnson > krona_tools
comparison classify_blast.xml @ 1:53258f6dddd3 draft
Add tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 29 Oct 2012 13:52:47 -0500 |
| parents | |
| children | 5f0f9a9b59e3 |
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| 0:f8fdde273a2a | 1:53258f6dddd3 |
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| 1 <tool id="classify_blast" name="Classify BLAST" version="1.0.0"> | |
| 2 <description>results using KronaTools</description> | |
| 3 <command> | |
| 4 ktClassifyBLAST | |
| 5 -o $output | |
| 6 -e $factor | |
| 7 $random | |
| 8 #if $score == 'percentIdentity': | |
| 9 -p | |
| 10 #elif $score == 'bitScore': | |
| 11 -b | |
| 12 #end if | |
| 13 $summarize | |
| 14 #for $input in $inputs | |
| 15 ${input.input} | |
| 16 #end for | |
| 17 </command> | |
| 18 | |
| 19 <inputs> | |
| 20 <repeat name="inputs" title="BLAST result"> | |
| 21 <param name="input" format="tabular" type="data" label="BLAST result"/> | |
| 22 </repeat> | |
| 23 <param name="factor" type="float" value="10" label="E-value factor" help="For each query, hits with e-values within this factor of the best hit's e-value will be included when computing the lowest common ancestor (or picking randomly)."/> | |
| 24 <param name="random" type="boolean" truevalue="-r" falsevalue="" label="Random" help="Pick from hits within E-value factor randomly instead of finding the lowest common ancestor"/> | |
| 25 <param name="score" type="select" label="Score by"> | |
| 26 <option value="evalue">E-value</option> | |
| 27 <option value="percentIdentity">Percent identity</option> | |
| 28 <option value="bitScore">Bit score</option> | |
| 29 </param> | |
| 30 <param name="summarize" type="boolean" truevalue="-s" falsevalue="" label="Summarize" help="Sum results by taxonomy ID and list totals in the first column instead of query IDs"/> | |
| 31 </inputs> | |
| 32 | |
| 33 <outputs> | |
| 34 <data format="tabular" name="output"/> | |
| 35 </outputs> | |
| 36 | |
| 37 <help> | |
| 38 | |
| 39 **What it does** | |
| 40 | |
| 41 Creates taxonomic classifications for each query in BLAST results by finding the lowest common ancestor (or by picking randomly, if specified) of "best" hits (as determined by e-value factor above). Requires a KronaTools_ installation (2.0 or higher) with taxonomy downloaded. | |
| 42 | |
| 43 .. _KronaTools: http://krona.sourceforge.net | |
| 44 | |
| 45 **Input** | |
| 46 | |
| 47 Tabular BLAST results containing gi numbers. If comment lines are present, queries with no hits will be assigned to taxon -1 (consistent with MEGAN). | |
| 48 | |
| 49 Example input (BLAST):: | |
| 50 | |
| 51 1 2 3 4 5 6 7 8 9 10 11 12 | |
| 52 read1 gi|211853080|gb|EQ846228.1| 97.33 150 1 3 6 154 9518999 9519146 5e-64 252 | |
| 53 read2 gi|211853080|gb|EQ846228.1| 96.69 151 0 5 6 154 9496147 9496294 2e-62 246 | |
| 54 | |
| 55 **Output** | |
| 56 | |
| 57 The output is a list of query IDs (or counts, if **summarize** is specified) followed by NCBI taxonomy IDs and scores. This can be used to create a Krona chart by specifying "Taxonomy ID list" as the **input type**. If the output is summarized, the **summarized** option must also be specified when creating the chart. | |
| 58 | |
| 59 Example output (default):: | |
| 60 | |
| 61 1 (query ID) 2 (tax ID) 3 (score) | |
| 62 read1 9606 94.34 | |
| 63 read2 9616 32.17 | |
| 64 | |
| 65 Example output (summarized):: | |
| 66 | |
| 67 1 (count) 2 (tax ID) 3 (score) | |
| 68 243 9606 94.34 | |
| 69 17 9616 32.17 | |
| 70 | |
| 71 </help> | |
| 72 <requirements> | |
| 73 <requirement type="binary">ktClassifyBLAST</requirement> | |
| 74 </requirements> | |
| 75 </tool> |