Mercurial > repos > peterjc > blastxml_to_top_descr
changeset 18:5737e2e7179a draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr commit 21f6d9932d322034e4cea5fee23b24bf0b1e1e85-dirty
| author | peterjc |
|---|---|
| date | Thu, 18 May 2017 12:44:22 -0400 |
| parents | ccf0a59e8537 |
| children | a89d62b8a239 |
| files | tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.xml |
| diffstat | 2 files changed, 10 insertions(+), 11 deletions(-) [+] |
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--- a/tools/blastxml_to_top_descr/README.rst Thu May 18 07:40:03 2017 -0400 +++ b/tools/blastxml_to_top_descr/README.rst Thu May 18 12:44:22 2017 -0400 @@ -73,6 +73,8 @@ v0.1.1 - Embed citation information in the tool XML (new Galaxy feature). v0.1.2 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Thu May 18 07:40:03 2017 -0400 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Thu May 18 12:44:22 2017 -0400 @@ -1,22 +1,19 @@ <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.2"> <description>Make a table from BLAST output</description> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> - <command interpreter="python"> -blastxml_to_top_descr.py --f "$input.in_format" + <version_command> +python $__tool_directory__/blastxml_to_top_descr.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/blastxml_to_top_descr.py +-f '$input.in_format' #if $input.in_format == "tabular": --qseqid $input.qseqid --sseqid $input.sseqid --salltitles $input.salltitles #end if --o "${tabular_file}" +-o '${tabular_file}' -t ${topN} -"${in_file}" +'${in_file}' </command> <inputs> <conditional name="input">