Mercurial > repos > peterjc > sample_seqs
changeset 7:86710edcec02 draft
v0.2.5 use <command detect_errors="aggressive"> and other internal changes
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 12:20:59 -0400 |
| parents | 31f5701cd2e9 |
| children | 7c40a1fbc82e |
| files | tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.xml |
| diffstat | 2 files changed, 11 insertions(+), 12 deletions(-) [+] |
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--- a/tools/sample_seqs/README.rst Thu May 11 07:24:38 2017 -0400 +++ b/tools/sample_seqs/README.rst Thu May 11 12:20:59 2017 -0400 @@ -73,6 +73,8 @@ - Clarify paired read example in help text. v0.2.4 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. - Style changes to Python code (internal change only). +v0.2.5 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/sample_seqs/sample_seqs.xml Thu May 11 07:24:38 2017 -0400 +++ b/tools/sample_seqs/sample_seqs.xml Thu May 11 12:20:59 2017 -0400 @@ -1,22 +1,19 @@ -<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.4"> +<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.5"> <description>e.g. to reduce coverage</description> <requirements> <requirement type="package" version="1.67">biopython</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">sample_seqs.py --version</version_command> - <command interpreter="python"> -sample_seqs.py -f "$input_file.ext" -i "$input_file" -o "$output_file" + <version_command> +python $__tool_directory__/sample_seqs.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/sample_seqs.py -f '$input_file.ext' -i '$input_file' -o '$output_file' #if str($sampling.type) == "everyNth": --n "${sampling.every_n}" +-n '${sampling.every_n}' #elif str($sampling.type) == "percentage": --p "${sampling.percent}" +-p '${sampling.percent}' #else --c "${sampling.count}" +-c '${sampling.count}' #end if #if $interleaved --interleaved