Mercurial > repos > peterjc > seq_primer_clip
changeset 14:6abe3913c881 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty
| author | peterjc |
|---|---|
| date | Fri, 21 Apr 2017 12:07:00 -0400 |
| parents | 64cc41c3456d |
| children | 2ff23f071f32 |
| files | tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.xml |
| diffstat | 2 files changed, 8 insertions(+), 10 deletions(-) [+] |
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--- a/tools/seq_primer_clip/README.rst Thu Feb 09 11:27:30 2017 -0500 +++ b/tools/seq_primer_clip/README.rst Fri Apr 21 12:07:00 2017 -0400 @@ -69,8 +69,10 @@ - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - Fixed input file help text. -v0.0.14 - Updated to point at Biopython 1.67 (latest version in Tool Shed). +v0.0.14 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. - Explicit dependency on ``galaxy_sequence_utils``. + - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only) ======= ======================================================================
--- a/tools/seq_primer_clip/seq_primer_clip.xml Thu Feb 09 11:27:30 2017 -0500 +++ b/tools/seq_primer_clip/seq_primer_clip.xml Fri Apr 21 12:07:00 2017 -0400 @@ -3,16 +3,12 @@ <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_primer_clip.py --version</version_command> - <command interpreter="python"> -seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file + <version_command> +python $__tool_directory__/seq_primer_clip.py --version + </version_command> + <command detect_errors="aggresive"> +python $__tool_directory__/seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file </command> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/>