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changeset 27:61f402b6e240 draft

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Uploaded v0.0.20 preview 17, adding citation information.
author peterjc
date Wed, 11 Sep 2013 06:26:20 -0400
parents 946749c8605f
children 4ae1bac976f3
files 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
diffstat 12 files changed, 128 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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).
 ======= ======================================================================
 
 
--- 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
@@ -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>
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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