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changeset 49:17f84d08f5a6 draft

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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit f3980e76fb3b06f9c631e668f63f65055fc92cae-dirty"
author peterjc
date Tue, 08 Sep 2020 20:58:48 +0000
parents 25f86a96c4c9
children 8146c9884047
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
diffstat 17 files changed, 35 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/tools/ncbi_blast_plus/README.rst	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/README.rst	Tue Sep 08 20:58:48 2020 +0000
@@ -130,6 +130,23 @@
 History
 =======
 
+The wrappers now follow the Galaxy convention of underlying tool version with
+a galaxy specific suffix which gets reset to zero with each new BLAST version:
+
+============== ===============================================================
+Version        Changes
+-------------- ---------------------------------------------------------------
+2.7.1+galaxy0  - Adopted BLAST version with integer Galaxy wrapper suffix.
+               - Dropped legacy ``repository_dependencies.xml`` and
+                 ``tool_dependencies.xml`` files. Instead assumes conda for
+                 dependency resolution and requires at least Galaxy v16.10
+                 which includes the BLAST datatypes.
+               - ``blastdbcmd`` wrapper supports multiple databases
+============== ===============================================================
+
+Prior releases used a self-contained version number (deliberately kept low to
+avoid any confusion with the NCBI BLAST version numbers):
+
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Convert BLAST XML output to tabular</description>
     <macros>
         <import>ncbi_macros.xml</import>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Show BLAST database information from blastdbcmd</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Extract sequence(s) from BLAST database</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
     <macros>
         <token name="@BINARY@">blastn</token>
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Search protein database with protein query sequence(s)</description>
     <macros>
         <token name="@BINARY@">blastp</token>
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Search protein database with translated nucleotide query sequence(s)</description>
     <macros>
         <token name="@BINARY@">blastx</token>
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <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	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo -->
     <description>masks low complexity regions</description>
     <macros>
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,5 +1,6 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">0.3.3</token>
+    <token name="@TOOL_VERSION@">2.7.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">16.10</token>
     <xml name="parallelism">
         <!-- If job splitting is enabled, break up the query file into parts -->
@@ -8,7 +9,7 @@
 
     <xml name="preamble">
         <requirements>
-            <requirement type="package" version="2.7.1">blast</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">blast</requirement>
         </requirements>
         <version_command>@BINARY@ -version</version_command>
     </xml>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Make BLAST database</description>
     <macros>
         <token name="@BINARY@">makeblastdb</token>
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Make profile database</description>
     <macros>
         <token name="@BINARY@">makeprofiledb</token>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Search protein domain database (PSSMs) with protein query sequence(s)</description>
     <macros>
         <token name="@BINARY@">deltablast</token>
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description>
     <macros>
         <token name="@BINARY@">rpstblastn</token>
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>low-complexity regions in protein sequences</description>
     <macros>
         <token name="@BINARY@">segmasker</token>
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Search translated nucleotide database with protein query sequence(s)</description>
     <macros>
         <token name="@BINARY@">tblastn</token>
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Tue Sep 08 16:38:13 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Tue Sep 08 20:58:48 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
     <macros>
         <token name="@BINARY@">tblastx</token>