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changeset 47:00330a63ffcf draft

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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty"
author peterjc
date Fri, 21 Aug 2020 12:44:41 +0000
parents 8ba7f30e8340
children 25f86a96c4c9
files 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 16 files changed, 16 insertions(+), 15 deletions(-) [+]
line wrap: on
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--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@WRAPPER_VERSION@">
+<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@WRAPPER_VERSION@">
+<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@WRAPPER_VERSION@">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="@WRAPPER_VERSION@">
+<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@WRAPPER_VERSION@">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@WRAPPER_VERSION@">
+<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@WRAPPER_VERSION@">
+<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,5 +1,6 @@
 <macros>
     <token name="@WRAPPER_VERSION@">0.3.3</token>
+    <token name="@PROFILE@">16.10</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" />
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@WRAPPER_VERSION@">
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@WRAPPER_VERSION@" profile="@PROFILE@">
     <description>Make BLAST database</description>
     <macros>
         <token name="@BINARY@">makeblastdb</token>
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@WRAPPER_VERSION@">
+<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@WRAPPER_VERSION@" profile="@PROFILE@">
     <description>Make profile database</description>
     <macros>
         <token name="@BINARY@">makeprofiledb</token>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@WRAPPER_VERSION@">
+<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@WRAPPER_VERSION@">
+<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="@WRAPPER_VERSION@">
+<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@WRAPPER_VERSION@">
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="@WRAPPER_VERSION@" 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	Thu Aug 20 20:17:51 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Fri Aug 21 12:44:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@WRAPPER_VERSION@">
+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="@WRAPPER_VERSION@" profile="@PROFILE@">
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
     <macros>
         <token name="@BINARY@">tblastx</token>