Mercurial > repos > artbio > snvtocnv
changeset 3:15b26e44b18d draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8-dirty"
| author | artbio |
|---|---|
| date | Fri, 19 Feb 2021 15:22:05 +0000 |
| parents | 9265faa93098 |
| children | e299c477b475 |
| files | snvtocnv.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/snvtocnv.xml Fri Feb 19 14:56:45 2021 +0000 +++ b/snvtocnv.xml Fri Feb 19 15:22:05 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.2"> +<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.2.1"> <description> </description> <macros> @@ -23,8 +23,8 @@ #else: ln -s $input_snvs input_snv.vcf && #end if - sequenza-utils gc_wiggle --fasta reference.fa -o reference.gc50Base.wig.gz -w 50 && - sequenza-utils snp2seqz -v '$input_snvs' -gc reference.gc50Base.wig.gz -o sample.seqz.gz && + sequenza-utils gc_wiggle --fasta reference.fa -o $refwig -w 50 && + sequenza-utils snp2seqz -v '$input_snvs' -gc $refwig -o sample.seqz.gz && sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o '$wiggle' && Rscript $__tool_directory__/segmentation_sequenza.R -i '$wiggle' @@ -45,7 +45,8 @@ </param> </inputs> <outputs> - <data name="wiggle" format="binary" label="binned wiggle" /> + <data name="refwig" format="txt" label="reference_wig" /> + <data name="wiggle" format="txt" label="binned wiggle" /> <data name="sample_segment" format="txt" label="sample segments" from_work_dir="test/sample_segments.txt" /> <data name="alt_solutions" format="txt" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" /> <data name="cnvs" format="tabular" label="Annotated CNVs" />