| Previous changeset 14:fb9cc7c43c22 (2013-05-02) Next changeset 16:2d4757de6180 (2013-05-20) |
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Commit message:
Uploaded v0.0.20 preview 6, adding links to the Tool Shed. |
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modified:
tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blast_plus.txt tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -129,5 +129,9 @@ low complexity (columns 21 and 22), and thus also calculated figures like the percentage identity (column 3). +**References** + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_blast_plus.txt --- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu May 02 13:21:42 2013 -0400 |
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| @@ -14,6 +14,9 @@ My thanks to Dannon Baker from the Galaxy development team for his assistance with this. +These wrappers are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + Automated Installation ====================== @@ -105,6 +108,7 @@ - Automatic installation via the Tool Shed now uses the NCBI provided precompiled binaries for 64bit Linux, rather than compiling locally. - Fallback on ElementTree if cElementTree missing in XML to tabular. + - Link to Tool Shed added to help text and this documentation. Developers |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.6"> <description>Show BLAST database information from blastdbcmd</description> <requirements> <requirement type="binary">blastdbcmd</requirement> @@ -61,5 +61,7 @@ Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.5"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.6"> <description>Extract sequence(s) from BLAST database</description> <requirements> <requirement type="binary">blastdbcmd</requirement> @@ -133,5 +133,7 @@ Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -247,5 +247,7 @@ Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.19"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.20"> <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -302,5 +302,7 @@ Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -288,5 +288,7 @@ Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.4"> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.5"> <description>Make BLAST database</description> <requirements> <requirement type="binary">makeblastdb</requirement> @@ -118,5 +118,12 @@ **Documentation** http://www.ncbi.nlm.nih.gov/books/NBK1763/ + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.3"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.4"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> @@ -232,5 +232,7 @@ Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.3"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.4"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> @@ -233,5 +233,7 @@ Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.19"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.20"> <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -334,5 +334,7 @@ Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
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| diff -r fb9cc7c43c22 -r c19e1150779d tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu May 02 11:21:54 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu May 02 13:21:42 2013 -0400 |
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| @@ -288,5 +288,7 @@ Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |