Mercurial > repos > sanbi-uwc > qc
changeset 5:499b71c93c5d draft
"planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/qc commit c11a408ecf1ea81fcca4bac8d503ee2731077722-dirty"
| author | sanbi-uwc |
|---|---|
| date | Wed, 07 Apr 2021 22:07:00 +0000 |
| parents | e34ab51fa707 |
| children | 878f18249f76 |
| files | qc.xml |
| diffstat | 1 files changed, 3 insertions(+), 15 deletions(-) [+] |
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--- a/qc.xml Thu Apr 01 07:57:59 2021 +0000 +++ b/qc.xml Wed Apr 07 22:07:00 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="qc_cog_uk" name="Quality Control (COG-UK QC)" version="0.1.0" python_template_version="3.5"> +<tool id="qc_cog_uk" name="Quality Control (COG-UK QC)" version="0.1.1" python_template_version="3.5"> <requirements> <requirement type="package" version="1.11">samtools</requirement> <requirement type="package" version="1.78">biopython</requirement> @@ -8,25 +8,13 @@ <command detect_errors="exit_code" interpreter="python"><![CDATA[ qc.py '$qc_type_conditional.qc_type' --outfile '$output1' - --sample '$input_sample' + --sample 'sample' --ref '$input_ref' --bam '$input_bam' --fasta '$input_cons_fasta' && - mv '$input_sample'.depth.png '$output2' + mv sample.depth.png '$output2' ]]></command> <inputs> - <conditional name="input_type_conditional"> - <param name="input_type" type="select" label="Input Type"> - <option value="single" selected="true">Single Dataset</option> - <option value="paired_collection">Paired Collection</option> - </param> - <when value="single"> - <param name="input_sample" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/> - </when> - <when value="paired_collection"> - <param name="input_sample" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/> - </when> - </conditional> <conditional name="qc_type_conditional"> <param name="qc_type" type="select" label="Input Type"> <option value="--illumina" selected="true">Illumina</option>