Mercurial > repos > peterjc > seq_rename
changeset 20:a7de1d3c3148 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty
| author | peterjc |
|---|---|
| date | Fri, 21 Apr 2017 12:07:26 -0400 |
| parents | 412e708d0172 |
| children | 5f87e696d49c |
| files | tools/seq_rename/README.rst tools/seq_rename/seq_rename.xml |
| diffstat | 2 files changed, 8 insertions(+), 10 deletions(-) [+] |
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--- a/tools/seq_rename/README.rst Fri Feb 03 12:55:57 2017 -0500 +++ b/tools/seq_rename/README.rst Fri Apr 21 12:07:26 2017 -0400 @@ -82,6 +82,8 @@ v0.0.8 - Updated to point at Biopython 1.67 (latest version in Tool Shed). - Explicit dependency on ``galaxy_sequence_utils``. - Python style updates (internal change only). +v0.0.9 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/seq_rename/seq_rename.xml Fri Feb 03 12:55:57 2017 -0500 +++ b/tools/seq_rename/seq_rename.xml Fri Apr 21 12:07:26 2017 -0400 @@ -1,18 +1,14 @@ -<tool id="seq_rename" name="Rename sequences" version="0.0.8"> +<tool id="seq_rename" name="Rename sequences" version="0.0.9"> <description>with ID mapping from a tabular file</description> <requirements> <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> <requirement type="package" version="1.67">biopython</requirement> - <requirement type="python-module">Bio</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">seq_rename.py --version</version_command> - <command interpreter="python"> -seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file + <version_command> +python $__tool_directory__/seq_rename.py --version +</version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/seq_rename.py '$input_tabular' '$old_column' '$new_column' '$input_file' '$input_file.ext' '$output_file' </command> <inputs> <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />