Mercurial > repos > peterjc > blast_rbh
changeset 33:692366540172 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 21f6d9932d322034e4cea5fee23b24bf0b1e1e85-dirty
author | peterjc |
---|---|
date | Thu, 18 May 2017 12:43:55 -0400 |
parents | b662383a4bdc |
children | 362c62ef2feb |
files | tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml |
diffstat | 2 files changed, 8 insertions(+), 11 deletions(-) [+] |
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--- a/tools/blast_rbh/README.rst Thu May 18 07:39:37 2017 -0400 +++ b/tools/blast_rbh/README.rst Thu May 18 12:43:55 2017 -0400 @@ -91,6 +91,8 @@ v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda. - Update Biopython dependency. - Tweak Python script to work under Python 2 or Python 3. +v0.1.12 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/blast_rbh/blast_rbh.xml Thu May 18 07:39:37 2017 -0400 +++ b/tools/blast_rbh/blast_rbh.xml Thu May 18 12:43:55 2017 -0400 @@ -1,19 +1,14 @@ -<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11"> +<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.12"> <description>from two FASTA files</description> <requirements> <requirement type="package" version="1.67">biopython</requirement> <requirement type="package" version="2.5.0">blast</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python"> -blast_rbh.py --version + <version_command> +python $__tool_directory__/blast_rbh.py --version </version_command> - <command interpreter="python"> -blast_rbh.py "$fasta_a" "$fasta_b" + <command detect_errors="aggressive"> +python $__tool_directory__/blast_rbh.py '$fasta_a' '$fasta_b' -a $seq.dbtype #if $seq.dbtype=="nucl" -t $seq.nucl_type @@ -23,7 +18,7 @@ $make_nr -i $identity -c $q_cover --o "$output" +-o '$output' </command> <inputs> <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->