Mercurial > repos > peterjc > samtools_idxstats
changeset 10:515fc5316fdb draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 12:48:26 -0400 |
| parents | b0ac04e1efe0 |
| children | 6955e091c023 |
| files | tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml |
| diffstat | 2 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/tools/samtools_idxstats/README.rst Wed May 10 12:48:16 2017 -0400 +++ b/tools/samtools_idxstats/README.rst Thu May 11 12:48:26 2017 -0400 @@ -54,6 +54,8 @@ v0.0.3 - Embed samtools citation in tool XML. v0.0.4 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.0.5 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/samtools_idxstats/samtools_idxstats.xml Wed May 10 12:48:16 2017 -0400 +++ b/tools/samtools_idxstats/samtools_idxstats.xml Thu May 11 12:48:26 2017 -0400 @@ -1,15 +1,14 @@ -<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4"> +<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.5"> <description>samtools idxstats</description> <requirements> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">samtools_idxstats.py --version</version_command> - <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command> + <version_command> +python $__tool_directory__/samtools_idxstats.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/samtools_idxstats.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' + </command> <inputs> <param name="input_bam" type="data" format="bam" label="Input BAM file" /> </inputs>