Mercurial > repos > peterjc > blastxml_to_top_descr
annotate tools/ncbi_blast_plus/blastxml_to_top_descr.xml @ 7:a7add03a44fd draft
Uploaded v0.0.6, checks return code for error handling
| author | peterjc |
|---|---|
| date | Wed, 17 Apr 2013 11:46:03 -0400 |
| parents | 8a0771c5e236 |
| children | a8ef75aab1f9 |
| rev | line source |
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Uploaded v0.0.6, checks return code for error handling
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1 <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.6"> |
| 0 | 2 <description>Make a table from BLAST XML</description> |
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Uploaded v0.0.5, reports number of queries with hits in stdout (peek text).
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3 <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> |
| 0 | 4 <command interpreter="python"> |
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5 blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN} |
| 0 | 6 </command> |
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Uploaded v0.0.6, checks return code for error handling
peterjc
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7 <stdio> |
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Uploaded v0.0.6, checks return code for error handling
peterjc
parents:
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8 <!-- Assume anything other than zero is an error --> |
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Uploaded v0.0.6, checks return code for error handling
peterjc
parents:
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9 <exit_code range="1:" /> |
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Uploaded v0.0.6, checks return code for error handling
peterjc
parents:
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10 <exit_code range=":-1" /> |
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a7add03a44fd
Uploaded v0.0.6, checks return code for error handling
peterjc
parents:
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11 </stdio> |
| 0 | 12 <inputs> |
| 13 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> | |
| 14 <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data name="tabular_file" format="tabular" label="Top $topN descriptions from $blastxml_file.name" /> | |
| 18 </outputs> | |
| 19 <requirements> | |
| 20 </requirements> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> | |
| 24 <param name="topN" value="3" /> | |
| 25 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" /> | |
| 26 </test> | |
| 27 </tests> | |
| 28 <help> | |
| 29 | |
| 30 **What it does** | |
| 31 | |
| 32 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of | |
| 33 formats including text, tabular and a more detailed XML format. You can | |
| 34 do a lot of things with tabular files in Galaxy (sorting, filtering, joins, | |
| 35 etc) however currently the BLAST tabular output omits the hit descriptions | |
| 36 found in the other output formats. | |
| 37 | |
| 38 This tool turns a BLAST XML file into a simple tabular file containing | |
| 39 one row per query sequence, containing the query identifier and then | |
| 40 the three (by default) top hit descriptions. If a query doesn't have | |
| 41 that many hits, then these entries are left blank. | |
| 42 | |
| 43 **Example Usage** | |
| 44 | |
| 45 One simple usage would be to take a transcriptome assembly or set of | |
| 46 gene predictions, run a BLAST search against the NCBI NR database, and | |
| 47 then use this tool to make a table of the top three BLAST hits. This | |
| 48 can give you a 'quick and dirty' crude annotation, potentially enough | |
| 49 to spot some problems (e.g. bacterial contaimination could be very | |
| 50 obvious). | |
| 51 | |
| 52 </help> | |
| 53 </tool> |