Mercurial > repos > peterjc > ncbi_blast_plus

changeset 15:c19e1150779d draft

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Uploaded v0.0.20 preview 6, adding links to the Tool Shed.
author peterjc
date Thu, 02 May 2013 13:21:42 -0400
parents fb9cc7c43c22
children 2d4757de6180
files 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
diffstat 12 files changed, 40 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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>
--- 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
@@ -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
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>
--- 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
@@ -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>