Mercurial > repos > peterjc > count_roi_variants
changeset 10:7a05cb080ea5 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 12:43:27 -0400 |
| parents | 4200518b0feb |
| children | cc86a2b3dc8e |
| files | tools/count_roi_variants/README.rst tools/count_roi_variants/count_roi_variants.xml |
| diffstat | 2 files changed, 11 insertions(+), 9 deletions(-) [+] |
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--- a/tools/count_roi_variants/README.rst Thu May 11 10:05:08 2017 -0400 +++ b/tools/count_roi_variants/README.rst Thu May 11 12:43:27 2017 -0400 @@ -80,6 +80,9 @@ v0.0.2 - Cope with pipes in reference name (e.g. NCBI style FASTA naming) v0.0.3 - Include a functional test for using an unrecognised reference. v0.0.4 - Improved usage text and README for use outside of Galaxy. +v0.0.5 - Fix samtools dependency version inconsistency, using v1.2 now. + - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/count_roi_variants/count_roi_variants.xml Thu May 11 10:05:08 2017 -0400 +++ b/tools/count_roi_variants/count_roi_variants.xml Thu May 11 12:43:27 2017 -0400 @@ -1,15 +1,14 @@ -<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.3"> +<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.5"> <description>using samtools view</description> <requirements> - <requirement type="package" version="1.2.2">samtools</requirement> + <requirement type="package" version="1.2">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">count_roi_variants.py --version</version_command> - <command interpreter="python">count_roi_variants.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular" "$region"</command> + <version_command> +python $__tool_directory__/count_roi_variants.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/count_roi_variants.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' '$region' + </command> <inputs> <param name="input_bam" type="data" format="bam" label="Input BAM file" /> <param name="region" type="text" label="Region of interest" help="Use the reference:start-end syntax as in samtools.">