Mercurial > repos > geert-vandeweyer > coverage_report
changeset 19:6c7b09220992 draft
new version 0.0.3 (fix on headless R)
| author | geert-vandeweyer |
|---|---|
| date | Thu, 06 Nov 2014 03:35:57 -0500 |
| parents | 43427b07e6bb |
| children | b8e4ed167120 |
| files | CoverageReport.xml readme.rst tool_dependencies.xml |
| diffstat | 3 files changed, 8 insertions(+), 13 deletions(-) [+] |
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--- a/CoverageReport.xml Wed Jun 18 08:18:10 2014 -0400 +++ b/CoverageReport.xml Thu Nov 06 03:35:57 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.2"> +<tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.3"> <description></description> <command interpreter="perl"> @@ -81,7 +81,7 @@ 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<space>Exon_number" : This is split on the space after 'GeneName' for correct grouping. + Column 4: Target Name. Use : "GENE-NAME|Exon_number" : This is split on the pipe (or space) after 'GeneName' for correct grouping.Example: "CLIP2|Exon_4" Column 5: Score : ignored, use '0' Column 6: Strand: ignored,'+' or '-'
--- a/readme.rst Wed Jun 18 08:18:10 2014 -0400 +++ b/readme.rst Thu Nov 06 03:35:57 2014 -0500 @@ -1,23 +1,18 @@ -Panel Resequencing Report -========================= - -This wrapper was created by Geert Vandeweyer. It is free to use, adapt and redistribute, but please mention the original source. +Panel Resequencing Report: This wrapper was created by Geert Vandeweyer. It is free to use, adapt and redistribute, but please mention the original source. -Installation -============ -The recommended installation is by means of the toolshed_. +Installation: The recommended installation is by means of the toolshed_. .. _toolshed: http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/coverage_report - Samtools, bedtools and R should be installed automatically by galaxy if not yet available. PdfLatex must be installed manually and added to the PATH. -History -======= +History: + 0.0.1 - Initial release, no dependency handling 0.0.2 - Updated release, following toolshed recommendations. +0.0.3 - Upgraded to R 3.0.3 (support on headless machines). Update to the documentation(targets bed format).
--- a/tool_dependencies.xml Wed Jun 18 08:18:10 2014 -0400 +++ b/tool_dependencies.xml Thu Nov 06 03:35:57 2014 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.0.2"> - <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="bedtools" version="2.18.2"> <repository changeset_revision="35905f2ae9f4" name="package_bedtools_2_18_2" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />