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changeset 17:697f40151eaf draft

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v0.1.05 - Update citation information now GigaScience paper is out
author peterjc
date Fri, 04 Sep 2015 09:45:57 -0400
parents b5f1f599d1fb
children 577d9c12411a
files tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.xml 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_convert2blastmask_wrapper.xml tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_makeprofiledb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml tools/ncbi_blast_plus/repository_dependencies.xml
diffstat 18 files changed, 37 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/tools/ncbi_blast_plus/README.rst	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Fri Sep 04 09:45:57 2015 -0400
@@ -26,11 +26,11 @@
 Citation
 ========
 
-Please cite the following paper (currently available as a preprint):
+Please cite the following paper:
 
 NCBI BLAST+ integrated into Galaxy.
 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
-bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint)
+GigaScience, 2015, 4:39 http://dx.doi.org/10.1186/s13742-015-0080-7
 
 You should also cite the NCBI BLAST+ tools:
 
@@ -218,6 +218,9 @@
 v0.1.04 - Fixed regression using BLAST databases from the history. Currently
           Galaxy inputs must still use ``.extra_files_path`` rather than the
           more consise ``.extra_files`` available for output files (Issue #69)
+v0.1.05 - Define ``parallelism`` tag via a macro (internal change only).
+        - Define wrapper versions via a macro (internal change only).
+        - Update citation information now GigaScience paper is out.
 ======= ======================================================================
 
 
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.05">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@">
     <description>Convert BLAST XML output to tabular</description>
     <stdio>
         <!-- Anything other than zero is an error -->
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.04">
+<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@WRAPPER_VERSION@">
     <description>Show BLAST database information from blastdbcmd</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.04">
+<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@WRAPPER_VERSION@">
     <description>Extract sequence(s) from BLAST database</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.04">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@WRAPPER_VERSION@">
     <description>Search nucleotide database with 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" merge_outputs="output1"></parallelism>
     <macros>
         <token name="@BINARY@">blastn</token>
         <import>ncbi_macros.xml</import>
     </macros>
+    <expand macro="parallelism" />
     <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.04">
+<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="@WRAPPER_VERSION@">
     <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" merge_outputs="output1" />
     <macros>
         <token name="@BINARY@">blastp</token>
         <import>ncbi_macros.xml</import>
     </macros>
+    <expand macro="parallelism" />
     <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.04">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@WRAPPER_VERSION@">
     <description>Search protein database 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" merge_outputs="output1"></parallelism>
     <macros>
         <token name="@BINARY@">blastx</token>
         <import>ncbi_macros.xml</import>
     </macros>
+    <expand macro="parallelism" />
     <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.04">
+<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@WRAPPER_VERSION@">
     <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description>
     <macros>
         <token name="@BINARY@">convert2blastmask</token>
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.04">
+<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@WRAPPER_VERSION@">
     <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo -->
     <description>masks low complexity regions</description>
     <macros>
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,9 @@
 <macros>
+    <token name="@WRAPPER_VERSION@">0.1.05</token>
+    <xml name="parallelism">
+        <!-- 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" merge_outputs="output1" />
+    </xml>
     <xml name="preamble">
         <requirements>
             <requirement type="binary">@BINARY@</requirement>
@@ -398,17 +403,12 @@
 #end if</token>
     <token name="@REFERENCES@">
 Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015).
-NCBI BLAST+ integrated into Galaxy. *BioRxiv* preprint.
-http://dx.doi.org/10.1101/014043
-
-Peter J.A. Cock, Björn A. Grüning, 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
+NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39
+http://dx.doi.org/10.1186/s13742-015-0080-7
 
 Christiam Camacho et al. (2009).
 BLAST+: architecture and applications.
-*BMC Bioinformatics*. 15;10:421.
+*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
@@ -417,10 +417,7 @@
     <xml name="blast_citations">
         <citations>
             <citation type="doi">10.1186/1471-2105-10-421</citation>
-            <citation type="doi">10.7717/peerj.167</citation>
-            <!-- TODO - remove PeerJ paper once "NCBI BLAST+ integrated into Galaxy" formally published? -->
-            <citation type="doi">10.1101/014043</citation>
-            <!-- TODO - Update DOI once "NCBI BLAST+ integrated into Galaxy" formally published -->
+            <citation type="doi">10.1186/s13742-015-0080-7</citation>
         </citations>
     </xml>
     <token name="@OUTPUT_FORMAT@">**Output format**
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.04">
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@WRAPPER_VERSION@">
     <description>Make BLAST database</description>
     <macros>
         <token name="@BINARY@">makeblastdb</token>
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.04">
+<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@WRAPPER_VERSION@">
     <description>Make profile database</description>
     <macros>
         <token name="@BINARY@">makeprofiledb</token>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.04">
+<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@WRAPPER_VERSION@">
     <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" merge_outputs="output1" />
     <macros>
         <token name="@BINARY@">deltablast</token>
         <import>ncbi_macros.xml</import>
     </macros>
+    <expand macro="parallelism" />
     <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.04">
+<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@WRAPPER_VERSION@">
     <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" merge_outputs="output1"></parallelism>
     <macros>
         <token name="@BINARY@">rpstblastn</token>
         <import>ncbi_macros.xml</import>
     </macros>
+    <expand macro="parallelism" />
     <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.04">
+<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="@WRAPPER_VERSION@">
     <description>low-complexity regions in protein sequences</description>
     <macros>
         <token name="@BINARY@">segmasker</token>
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.04">
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@WRAPPER_VERSION@">
     <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" merge_outputs="output1"></parallelism>
     <macros>
         <token name="@BINARY@">tblastn</token>
         <import>ncbi_macros.xml</import>
     </macros>
+    <expand macro="parallelism" />
     <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.04">
+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@WRAPPER_VERSION@">
     <description>Search translated nucleotide database 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" merge_outputs="output1"></parallelism>
     <macros>
         <token name="@BINARY@">tblastx</token>
         <import>ncbi_macros.xml</import>
     </macros>
+    <expand macro="parallelism" />
     <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
--- a/tools/ncbi_blast_plus/repository_dependencies.xml	Wed Jul 22 05:01:11 2015 -0400
+++ b/tools/ncbi_blast_plus/repository_dependencies.xml	Fri Sep 04 09:45:57 2015 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">
-    <repository changeset_revision="5482a8cd0f36" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="01b38f20197e" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>