| Previous changeset 26:946749c8605f (2013-08-15) Next changeset 28:4ae1bac976f3 (2013-09-12) |
|
Commit message:
Uploaded v0.0.20 preview 17, adding citation information. |
|
modified:
ncbi_blast_plus/README.rst ncbi_blast_plus/blastxml_to_tabular.xml ncbi_blast_plus/ncbi_blastdbcmd_info.xml ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml ncbi_blast_plus/ncbi_blastn_wrapper.xml ncbi_blast_plus/ncbi_blastp_wrapper.xml ncbi_blast_plus/ncbi_blastx_wrapper.xml ncbi_blast_plus/ncbi_makeblastdb.xml ncbi_blast_plus/ncbi_rpsblast_wrapper.xml ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml ncbi_blast_plus/ncbi_tblastn_wrapper.xml ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/README.rst --- a/ncbi_blast_plus/README.rst Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/README.rst Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -112,9 +112,11 @@ - Added percentage identity option to BLASTN. - Fallback on ElementTree if cElementTree missing in XML to tabular. - Link to Tool Shed added to help text and this documentation. - - Tweak dependency on blast_datatypes to also work on Test Tool Shed + - Tweak dependency on blast_datatypes to also work on Test Tool Shed. + - Dependency on new package_blast_plus_2_2_26 in Tool Shed. - Adopted standard MIT License. - Development moved to GitHub, https://github.com/peterjc/galaxy_blast + - Updated citation information (Cock et al. 2013). ======= ====================================================================== |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/blastxml_to_tabular.xml --- a/ncbi_blast_plus/blastxml_to_tabular.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/blastxml_to_tabular.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -131,6 +131,14 @@ **References** +If you use this Galaxy tool in work leading to a scientific publication please +cite: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + 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> |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -57,9 +57,18 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: -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. +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -129,9 +129,18 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: -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. +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -249,7 +249,18 @@ **References** -Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -298,9 +298,18 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: -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. +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -286,7 +286,18 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_makeblastdb.xml --- a/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -124,7 +124,18 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -230,7 +230,18 @@ **References** -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. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -231,7 +231,18 @@ **References** -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. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -332,7 +332,18 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |
| b |
| diff -r 946749c8605f -r 61f402b6e240 ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Aug 15 12:04:37 2013 -0400 +++ b/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Sep 11 06:26:20 2013 -0400 |
| b |
| @@ -286,7 +286,18 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 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 |