Mercurial > repos > iuc > mageck_gsea

diff test-data/out.pathway.log.txt @ 0:d95eae71878e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
author iuc
date Wed, 14 Feb 2018 06:41:59 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.pathway.log.txt	Wed Feb 14 06:41:59 2018 -0500
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+INFO  @ Mon, 12 Feb 2018 04:19:29: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck pathway --gene-ranking /tmp/tmpd9LSrs/files/000/dataset_19.dat --gmt-file /tmp/tmpd9LSrs/files/000/dataset_20.dat -n sample1 --method gsea --sort-criteria neg --ranking-column 2 --ranking-column-2 8 --pathway-alpha 0.25 --permutation 1000 
+INFO  @ Mon, 12 Feb 2018 04:19:29: Welcome to MAGeCK v0.5.7. Command: pathway 
+INFO  @ Mon, 12 Feb 2018 04:19:29: GSEA command for negative selection: mageckGSEA  -s  -c 2  -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat"  -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat"  -o sample1.pathway.low.txt  
+INFO  @ Mon, 12 Feb 2018 04:19:29: Running command: mageckGSEA  -s  -c 2  -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat"  -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat"  -o sample1.pathway.low.txt  
+INFO  @ Mon, 12 Feb 2018 04:19:29: Command message: 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   Output file: sample1.pathway.low.txt 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   pathway size:1 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   rank size:101 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   Permutations:1000 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   . 
+INFO  @ Mon, 12 Feb 2018 04:19:29:    
+INFO  @ Mon, 12 Feb 2018 04:19:29: End command message. 
+INFO  @ Mon, 12 Feb 2018 04:19:29: GSEA command for positive selection: mageckGSEA  -s  -c 8  -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat"  -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat"  -o sample1.pathway.high.txt  
+INFO  @ Mon, 12 Feb 2018 04:19:29: Running command: mageckGSEA  -s  -c 8  -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat"  -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat"  -o sample1.pathway.high.txt  
+INFO  @ Mon, 12 Feb 2018 04:19:29: Command message: 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   Output file: sample1.pathway.high.txt 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   pathway size:1 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   rank size:101 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   Permutations:1000 
+INFO  @ Mon, 12 Feb 2018 04:19:29:   . 
+INFO  @ Mon, 12 Feb 2018 04:19:29:    
+INFO  @ Mon, 12 Feb 2018 04:19:29: End command message. 
+INFO  @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.tmp 
+INFO  @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.tmp 
+INFO  @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.txt 
+INFO  @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.txt