Mercurial > repos > lecorguille > xcms_fillpeaks
changeset 5:cd351af95d14 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
| author | lecorguille |
|---|---|
| date | Mon, 25 Apr 2016 11:15:12 -0400 |
| parents | 2edfa5e1f719 |
| children | 465623d2f6fa |
| files | abims_xcms_fillPeaks.xml planemo_test.sh test-data/faahKO.xset.group.retcor.group.RData test-data/faahKO_reduce.zip test-data/log.txt test-data/sacuri_dir_root.zip test-data/xset.group.retcor.group.RData |
| diffstat | 7 files changed, 28 insertions(+), 60 deletions(-) [+] |
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--- a/abims_xcms_fillPeaks.xml Fri Apr 08 10:39:59 2016 -0400 +++ b/abims_xcms_fillPeaks.xml Mon Apr 25 11:15:12 2016 -0400 @@ -41,7 +41,7 @@ </outputs> <tests> - <test> + <!--<test> <param name="image" value="xset.group.retcor.group.RData"/> <param name="method" value="chrom"/> <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> @@ -55,6 +55,21 @@ <has_text text="Sample classes: bio, blank" /> </assert_contents> </output> + </test>--> + <test> + <param name="image" value="faahKO.xset.group.retcor.group.RData"/> + <param name="method" value="chrom"/> + <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 32720 (about 8180 per sample)" /> + <has_text text="Peak Groups: 8157" /> + <has_text text="Sample classes: KO, WT" /> + </assert_contents> + </output> </test> </tests>
--- a/planemo_test.sh Fri Apr 08 10:39:59 2016 -0400 +++ b/planemo_test.sh Mon Apr 25 11:15:12 2016 -0400 @@ -1,11 +1,10 @@ -planemo conda_init -planemo conda_install . -planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev" +# Example of planemo command to launch test -#All 1 test(s) executed passed. -#abims_xcms_fillPeaks[0]: passed +# 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-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh planemo test --install_galaxy --galaxy_branch "dev" @@ -14,8 +13,16 @@ #abims_xcms_fillPeaks[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 --galaxy_branch "dev" + +#All 1 test(s) executed passed. +#abims_xcms_fillPeaks[0]: passed +# -- Use of shed_test planemo shed_test --install_galaxy --galaxy_branch "dev" -t testtoolshed #All 1 test(s) executed passed. #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/2.0.6[0]: passed
--- a/test-data/log.txt Fri Apr 08 10:39:59 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ - PACKAGE INFO -parallel 3.2.2 -BiocGenerics 0.16.1 -Biobase 2.30.0 -Rcpp 0.12.2 -mzR 2.4.1 -xcms 1.44.0 -snow 0.4.1 -batch 1.1.4 - - - ARGUMENTS INFO -xfunction fillPeaks -image /tmp/tmpk97EMC/files/000/dataset_1.dat -xsetRdataOutput /tmp/tmpk97EMC/files/000/dataset_3.dat -method chrom -zipfile /tmp/tmpk97EMC/files/000/dataset_2.dat - - - INFILE PROCESSING INFO - - - ARGUMENTS PROCESSING INFO -files_root_directory sacuri -Compute md5 checksum... - - - MAIN PROCESSING INFO -sacuri/bio/HU_neg_017.mzXML -sacuri/bio/HU_neg_028.mzXML -sacuri/blank/Blanc04.mzXML -sacuri/blank/Blanc06.mzXML - - -null device - 1 - - - XSET OBJECT INFO -An "xcmsSet" object with 4 samples - -Time range: 0.2-1140.1 seconds (0-19 minutes) -Mass range: 50.0021-999.9863 m/z -Peaks: 199718 (about 49930 per sample) -Peak Groups: 48958 -Sample classes: bio, blank - -Profile settings: method = bin - step = 0.01 - -Memory usage: 27.3 MB - - - DONE