Mercurial > repos > lecorguille > camera_annotate
changeset 37:636e36a64d31 draft
planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
| author | lecorguille |
|---|---|
| date | Tue, 09 Apr 2019 11:36:39 -0400 |
| parents | b6a8143c397c |
| children | 2184c0435edf |
| files | README.rst abims_CAMERA_annotateDiffreport.xml lib.r macros.xml planemo_test.sh |
| diffstat | 5 files changed, 17 insertions(+), 43 deletions(-) [+] |
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--- a/README.rst Fri Feb 01 11:29:35 2019 -0500 +++ b/README.rst Tue Apr 09 11:36:39 2019 -0400 @@ -2,9 +2,10 @@ Changelog/News -------------- -**Version 2.2.5 - 01/02/2019** +**Version 2.2.5 - 09/04/2019** - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) **Version 2.2.4 - 09/10/2018**
--- a/abims_CAMERA_annotateDiffreport.xml Fri Feb 01 11:29:35 2019 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Tue Apr 09 11:36:39 2019 -0400 @@ -200,15 +200,15 @@ </data> <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf"> <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter> - <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" visible="true" /> + <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" /> </collection> - <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport.pdf" from_work_dir="tabular.zip"> + <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.pdf" from_work_dir="tabular.zip"> <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter> </data> <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table"> <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter> - <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" visible="true" /> + <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" /> </collection> </outputs> @@ -442,9 +442,12 @@ Changelog/News -------------- -**Version 2.2.5 - 01/02/2019** +.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS + +**Version 2.2.5 - 09/04/2019** - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) **Version 2.2.4 - 09/10/2018**
--- a/lib.r Fri Feb 01 11:29:35 2019 -0500 +++ b/lib.r Tue Apr 09 11:36:39 2019 -0400 @@ -36,13 +36,13 @@ #@author G. Le Corguille #The function create a zip archive from the different png generated by diffreport diffreport_png2zip <- function() { - zip("eic.zip",dir(pattern="_eic")) - zip("box.zip",dir(pattern="_box")) + zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip")) + zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip")) } #The function create a zip archive from the different tabular generated by diffreport diffreport_tabular2zip <- function() { - zip("tabular.zip",dir(pattern="tabular/*")) + zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip")) } #@author G. Le Corguille @@ -152,7 +152,7 @@ diffrep=diffrep[order(diffrep$pvalue), ] } - dir.create("tabular") + dir.create("tabular", showWarnings = FALSE) write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep="")) if (listArguments[["eicmax"]] != 0) {
--- a/macros.xml Fri Feb 01 11:29:35 2019 -0500 +++ b/macros.xml Tue Apr 09 11:36:39 2019 -0400 @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4_2">r-snow</requirement> - <requirement type="package" version="3.0.0">bioconductor-xcms</requirement> - <requirement type="package" version="1.34.0">bioconductor-camera</requirement> - <requirement type="package" version="2.28.0">bioconductor-multtest</requirement> + <requirement type="package" version="0.4_3">r-snow</requirement> + <requirement type="package" version="1.38.1">bioconductor-camera</requirement> + <requirement type="package" version="2.38.0">bioconductor-multtest</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="1.3.23">graphicsmagick</requirement> + <requirement type="package" version="1.3.26">graphicsmagick</requirement> </requirements> </xml> <xml name="stdio">
--- a/planemo_test.sh Fri Feb 01 11:29:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -# Example of planemo command to launch test - -# Note: --galaxy_branch "dev" is set to deal with zip file - - -# -- Use of installed package environments -# after having installing package on a local galaxy instance -source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh -source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh -planemo test --install_galaxy - -#All 1 test(s) executed passed. -#abims_CAMERA_annotateDiffreport[0]: passed - - -# -- Use of conda dependencies -planemo conda_init --conda_prefix /tmp/mc -planemo conda_install --conda_prefix /tmp/mc . -planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution - -#All 1 test(s) executed passed. -#abims_CAMERA_annotateDiffreport[0]: passed - - -# -- Use of shed_test -planemo shed_test --install_galaxy -t testtoolshed - -#All 1 test(s) executed passed. -#testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: passed