# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock@googlemail.com> # Date 1289925107 0 # Node ID 2e2ee0289d67d244954aa05bfe315dbb5ff413eb # Parent d2d0c199c20ddf942e1e2587dc9aede8acd9cebc Fix BLAST+ regression from changeset 535d276c92bc (loc file columns) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -40,10 +40,13 @@ blastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> - <!-- <options from_data_table="blastdb" /> --> + <!-- The BLAST loc file has three columns: + column 0 is an identifier (not used here, see legacy megablast wrapper), + column 1 is the caption (show this to the user), + column 2 is the database path (given to BLAST+) --><options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -41,10 +41,13 @@ blastp </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> - <!-- <options from_data_table="blastdb_p" /> --> + <!-- The BLAST loc file has three columns: + column 0 is an identifier (not used), + column 1 is the caption (show this to the user), + column 2 is the database path (given to BLAST+) --><options from_file="blastdb_p.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -39,10 +39,13 @@ tblastx </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> - <!-- <options from_data_table="blastdb" /> --> + <!-- The BLAST loc file has three columns: + column 0 is an identifier (not used here, see legacy megablast wrapper), + column 1 is the caption (show this to the user), + column 2 is the database path (given to BLAST+) --><options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -40,10 +40,13 @@ blastx </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> - <!-- <options from_data_table="blastdb_p" /> --> + <!-- The BLAST loc file has three columns: + column 0 is an identifier (not used), + column 1 is the caption (show this to the user), + column 2 is the database path (given to BLAST+) --><options from_file="blastdb_p.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -40,10 +40,13 @@ tblastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> - <!-- <options from_data_table="blastdb" /> --> + <!-- The BLAST loc file has three columns: + column 0 is an identifier (not used here, see legacy megablast wrapper), + column 1 is the caption (show this to the user), + column 2 is the database path (given to BLAST+) --><options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" />