Mercurial > repos > peterjc > blastxml_to_top_descr
changeset 12:b7c85bb42d87 draft
Uploaded v0.1.0b, fixed typo
| author | peterjc |
|---|---|
| date | Fri, 13 Jun 2014 07:06:23 -0400 |
| parents | 6f623a9718f1 |
| children | 796dc2ff8e8e |
| files | tools/blastxml_to_top_descr/blastxml_to_top_descr.xml tools/blastxml_to_top_descr/repository_dependencies.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Tue May 13 06:32:42 2014 -0400 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Fri Jun 13 07:06:23 2014 -0400 @@ -1,5 +1,5 @@ <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.0"> - <description>Make a table from BLAST XML</description> + <description>Make a table from BLAST output</description> <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> <command interpreter="python"> blastxml_to_top_descr.py @@ -72,7 +72,7 @@ formats including text, tabular and a more detailed XML format. You can do a lot of things with tabular files in Galaxy (sorting, filtering, joins, etc), however until BLAST+ 2.2.28 the tabular output never included the -hit descriptions (titles) found in the other output formats +hit descriptions (titles) found in the other output formats. This tool turns a BLAST XML file into a simple tabular file containing one row per query sequence, containing the query identifier and then @@ -82,7 +82,7 @@ This tool can also be used with the tabular output from BLAST+ instead, provided the relevant columns are provided. The default settings will work with the default 25 column extended output from the BLAST+ tools -wrapped in Galaxy. Note if a query has not hits, it does not appear in +wrapped in Galaxy. Note if a query has *no* hits, it does not appear in the BLAST tabular output. **Example Usage**
--- a/tools/blastxml_to_top_descr/repository_dependencies.xml Tue May 13 06:32:42 2014 -0400 +++ b/tools/blastxml_to_top_descr/repository_dependencies.xml Fri Jun 13 07:06:23 2014 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Requires BLAST XML and database datatype definitions."> -<repository changeset_revision="939a600f45e9" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +<repository changeset_revision="939a600f45e9" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>