Mercurial > repos > geert-vandeweyer > coverage_report
changeset 4:2799221681dd draft
Uploaded
| author | geert-vandeweyer |
|---|---|
| date | Thu, 13 Feb 2014 04:45:56 -0500 |
| parents | 39c374d4cba7 |
| children | 26a5b8623597 |
| files | CoverageReport.xml |
| diffstat | 1 files changed, 6 insertions(+), 12 deletions(-) [+] |
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--- a/CoverageReport.xml Thu Feb 13 04:45:48 2014 -0500 +++ b/CoverageReport.xml Thu Feb 13 04:45:56 2014 -0500 @@ -1,5 +1,6 @@ -<tool id="CoverageReport" name="Panel Coverage Report" version="0.0.2"> +<tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.2"> <description></description> + <command interpreter="perl"> CoverageReport.pl ## input files @@ -27,8 +28,9 @@ #end if </command> <requirements> - <requirement type="package">BEDTools</requirement> - <requirement type="package">samtools</requirement> + <requirement type="package" version="2.11.0">R</requirement> + <requirement type="package" version="2.18.2">bedtools</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="binary">pdflatex</requirement> </requirements> <inputs> @@ -80,7 +82,7 @@ Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1') Column 2: Start Position Column 3: End Position - Column 4: Target Name. Use : "GENE-NAME|Exon_number" : This is split on the 'Pipe' after 'GeneName' for correct grouping. + Column 4: Target Name. Use : "GENE-NAME<space>Exon_number" : This is split on the space after 'GeneName' for correct grouping. Column 5: Score : ignored, use '0' Column 6: Strand: ignored,'+' or '-' @@ -111,14 +113,6 @@ - Position in target region - Coverage at position ------- - -**Requirements** - - - BEDTools (from toolshed) - - Samtools (from toolshed) - - pdflatex : binary must be in path, to create the pdf report. - </help> </tool>