| Previous changeset 48:25f86a96c4c9 (2020-09-08) Next changeset 50:8146c9884047 (2020-09-09) |
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Commit message:
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit f3980e76fb3b06f9c631e668f63f65055fc92cae-dirty" |
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modified:
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 |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/README.rst --- 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 |
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| @@ -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 ------- ---------------------------------------------------------------------- |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/blastxml_to_tabular.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_macros.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_makeblastdb.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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 25f86a96c4c9 -r 17f84d08f5a6 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- 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 |
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| @@ -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> |