Mercurial > repos > jjohnson > krona_tools
annotate classify_blast.xml @ 3:3398919bc103 draft
Comment tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 29 Oct 2012 16:05:59 -0500 |
| parents | 5f0f9a9b59e3 |
| children |
| rev | line source |
|---|---|
| 1 | 1 <tool id="classify_blast" name="Classify BLAST" version="1.0.0"> |
| 2 <description>results using KronaTools</description> | |
|
2
5f0f9a9b59e3
Add package reqguirement for KronaTools
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
3 <requirements> |
|
5f0f9a9b59e3
Add package reqguirement for KronaTools
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
4 <requirement type="package" version="2.2">KronaTools</requirement> |
|
5f0f9a9b59e3
Add package reqguirement for KronaTools
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
5 </requirements> |
| 1 | 6 <command> |
| 7 ktClassifyBLAST | |
| 8 -o $output | |
| 9 -e $factor | |
| 10 $random | |
| 11 #if $score == 'percentIdentity': | |
| 12 -p | |
| 13 #elif $score == 'bitScore': | |
| 14 -b | |
| 15 #end if | |
| 16 $summarize | |
| 17 #for $input in $inputs | |
| 18 ${input.input} | |
| 19 #end for | |
| 20 </command> | |
| 21 | |
| 22 <inputs> | |
| 23 <repeat name="inputs" title="BLAST result"> | |
| 24 <param name="input" format="tabular" type="data" label="BLAST result"/> | |
| 25 </repeat> | |
| 26 <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)."/> | |
| 27 <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"/> | |
| 28 <param name="score" type="select" label="Score by"> | |
| 29 <option value="evalue">E-value</option> | |
| 30 <option value="percentIdentity">Percent identity</option> | |
| 31 <option value="bitScore">Bit score</option> | |
| 32 </param> | |
| 33 <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"/> | |
| 34 </inputs> | |
| 35 | |
| 36 <outputs> | |
| 37 <data format="tabular" name="output"/> | |
| 38 </outputs> | |
| 39 | |
| 40 <help> | |
| 41 | |
| 42 **What it does** | |
| 43 | |
| 44 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. | |
| 45 | |
| 46 .. _KronaTools: http://krona.sourceforge.net | |
| 47 | |
| 48 **Input** | |
| 49 | |
| 50 Tabular BLAST results containing gi numbers. If comment lines are present, queries with no hits will be assigned to taxon -1 (consistent with MEGAN). | |
| 51 | |
| 52 Example input (BLAST):: | |
| 53 | |
| 54 1 2 3 4 5 6 7 8 9 10 11 12 | |
| 55 read1 gi|211853080|gb|EQ846228.1| 97.33 150 1 3 6 154 9518999 9519146 5e-64 252 | |
| 56 read2 gi|211853080|gb|EQ846228.1| 96.69 151 0 5 6 154 9496147 9496294 2e-62 246 | |
| 57 | |
| 58 **Output** | |
| 59 | |
| 60 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. | |
| 61 | |
| 62 Example output (default):: | |
| 63 | |
| 64 1 (query ID) 2 (tax ID) 3 (score) | |
| 65 read1 9606 94.34 | |
| 66 read2 9616 32.17 | |
| 67 | |
| 68 Example output (summarized):: | |
| 69 | |
| 70 1 (count) 2 (tax ID) 3 (score) | |
| 71 243 9606 94.34 | |
| 72 17 9616 32.17 | |
| 73 | |
| 74 </help> | |
| 75 <requirements> | |
| 76 <requirement type="binary">ktClassifyBLAST</requirement> | |
| 77 </requirements> | |
| 78 </tool> |