Mercurial > repos > devteam > ncbi_blast_plus
changeset 31:0e3cf9594bb7 draft
Update with window size fix
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2022 12:15:44 +0000 |
| parents | acf4e47b734c |
| children | a52d2d93e595 |
| files | tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml |
| diffstat | 5 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/tools/ncbi_blast_plus/README.rst Tue Mar 29 14:54:02 2022 +0000 +++ b/tools/ncbi_blast_plus/README.rst Tue Jun 07 12:15:44 2022 +0000 @@ -136,6 +136,8 @@ ============== =============================================================== Version Changes -------------- --------------------------------------------------------------- +2.10.1+galaxy2 - Fixed ``dc-megablast`` option in ``ncbi_blastn_wrapper.xml`` + wrapper from inserting ``-window_size`` twice when executing. 2.10.1+galaxy1 - Add tool `NCBI get species taxids` that wraps NCBI's `get_species_taxids.sh` script (https://www.ncbi.nlm.nih.gov/books/NBK546209/).
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Tue Mar 29 14:54:02 2022 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Tue Jun 07 12:15:44 2022 +0000 @@ -3,6 +3,9 @@ <macros> <import>ncbi_macros.xml</import> </macros> + <requirements> + <requirement type="package" version="3.9">python</requirement> + </requirements> <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command> <command detect_errors="aggressive"> python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file'
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Mar 29 14:54:02 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jun 07 12:15:44 2022 +0000 @@ -30,7 +30,7 @@ @ADV_QCOV_HSP_PERC@ ## only use window size if dc-megablast mode is used #if ($blast_type == "dc-megablast"): --window_size @ADV_WINDOW_SIZE@ + @ADV_WINDOW_SIZE@ #end if @ADV_GAPOPEN@ @ADV_GAPEXTEND@
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Tue Mar 29 14:54:02 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Tue Jun 07 12:15:44 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.10.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">16.10</token> <xml name="parallelism"> <!-- If job splitting is enabled, break up the query file into parts --> @@ -10,6 +10,7 @@ <xml name="preamble"> <requirements> <requirement type="package" version="@TOOL_VERSION@">blast</requirement> + <yield /> </requirements> <version_command>@BINARY@ -version</version_command> </xml>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Tue Mar 29 14:54:02 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Tue Jun 07 12:15:44 2022 +0000 @@ -4,7 +4,9 @@ <token name="@BINARY@">makeblastdb</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="preamble" /> + <expand macro="preamble"> + <requirement type="package" version="3.9">python</requirement> + </expand> <command detect_errors="aggressive" strict="true"><![CDATA[ python $__tool_directory__/check_no_duplicates.py ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)