| Previous changeset 6:0888f7ef739a (2016-04-08) Next changeset 8:53923784176c (2016-07-04) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 |
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modified:
abims_xcms_xcmsSet.xml planemo_test.sh |
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added:
test-data/faahKO_reduce.zip |
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removed:
test-data/sacuri_current_root.zip test-data/sacuri_dir_root.log.txt test-data/sacuri_dir_root.zip |
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| diff -r 0888f7ef739a -r 451ff602a957 abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Fri Apr 08 10:38:52 2016 -0400 +++ b/abims_xcms_xcmsSet.xml Mon Apr 25 11:14:02 2016 -0400 |
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| @@ -183,7 +183,7 @@ </outputs> <tests> - <test> + <!--<test> <param name="inputs|input" value="zip_file" /> <param name="inputs|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> <param name="methods|method" value="matchedFilter" /> @@ -203,7 +203,7 @@ <has_text text="Sample classes: bio, blank" /> </assert_contents> </output> - </test> + </test> <test> <param name="inputs|input" value="zip_file" /> <param name="inputs|zip_file" value="sacuri_current_root.zip" ftype="zip" /> @@ -220,6 +220,23 @@ <has_text text="Sample classes: bio, blank" /> </assert_contents> </output> + </test>--> + <test> + <param name="inputs|input" value="zip_file" /> + <param name="inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <param name="methods|method" value="centWave" /> + <param name="methods|ppm" value="25" /> + <param name="methods|peakwidth" value="20,50" /> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 9251 (about 2313 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: KO, WT" /> + </assert_contents> + </output> </test> </tests> |
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| diff -r 0888f7ef739a -r 451ff602a957 planemo_test.sh --- a/planemo_test.sh Fri Apr 08 10:38:52 2016 -0400 +++ b/planemo_test.sh Mon Apr 25 11:14:02 2016 -0400 |
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| @@ -1,18 +1,33 @@ -planemo conda_init -planemo conda_install . -planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev" +# 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-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh +planemo test --install_galaxy --galaxy_branch "dev" #All 2 test(s) executed passed. #abims_xcms_xcmsSet[0]: passed #abims_xcms_xcmsSet[1]: passed - - -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" +# -- 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 2 test(s) executed passed. #abims_xcms_xcmsSet[0]: passed -#abims_xcms_xcmsSet[1]: passed \ No newline at end of file +#abims_xcms_xcmsSet[1]: passed + + +# -- Use of shed_test +planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch ="dev" + +#All 2 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[0]: passed +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[1]: passed + |
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| diff -r 0888f7ef739a -r 451ff602a957 test-data/faahKO_reduce.zip |
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| Binary file test-data/faahKO_reduce.zip has changed |
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| diff -r 0888f7ef739a -r 451ff602a957 test-data/sacuri_current_root.zip |
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| Binary file test-data/sacuri_current_root.zip has changed |
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| diff -r 0888f7ef739a -r 451ff602a957 test-data/sacuri_dir_root.log.txt --- a/test-data/sacuri_dir_root.log.txt Fri Apr 08 10:38:52 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,67 +0,0 @@\n-\tPACKAGE INFO\n-parallel\t3.2.2\n-BiocGenerics\t0.16.1\n-Biobase\t2.30.0\n-Rcpp\t0.12.2\n-mzR\t2.4.1\n-xcms\t1.44.0\n-snow\t0.4.1\n-batch\t1.1.4\n-\n-\n-\tARGUMENTS INFO\n-zipfile\t/tmp/tmpAmhDSv/files/000/dataset_1.dat\n-xfunction\txcmsSet\n-xsetRdataOutput\t/tmp/tmpAmhDSv/files/000/dataset_2.dat\n-sampleMetadataOutput\t/tmp/tmpAmhDSv/files/000/dataset_3.dat\n-ticspdf\t/tmp/tmpAmhDSv/files/000/dataset_4.dat\n-bicspdf\t/tmp/tmpAmhDSv/files/000/dataset_5.dat\n-nSlaves\t1\n-method\tmatchedFilter\n-step\t0.01\n-fwhm\t4\n-max\t50\n-snthresh\t1\n-steps\t2\n-\n-\n-\tINFILE PROCESSING INFO\n-\n-\n-\tARGUMENTS PROCESSING INFO\n-files_root_directory\t sacuri \n-Compute md5 checksum...\n-Checking XML structure...\n-Checking files filenames compatibilities with xmcs...\n-\n-\n-\tMAIN PROCESSING INFO\n-55:579 60:1264 65:1988 70:2602 75:3287 80:3894 85:4629 90:5499 95:6174 100:6672 105:7194 110:7737 115:8205 120:8673 125:9117 130:9532 135:9973 140:10562 145:10945 150:11380 155:11788 160:12163 165:12477 170:12835 175:13276 180:13632 185:14142 190:14489 195:15022 200:15360 205:15716 210:15992 215:16297 220:16669 225:16895 230:17227 235:17487 240:17657 245:17956 250:18238 255:18464 260:18779 265:18969 270:19194 275:19503 280:19798 285:20041 290:20282 295:20498 300:20673 305:21027 310:21220 315:21403 320:21881 325:22431 330:22630 335:22775 340:22969 345:23144 350:23282 355:23425 360:24001 365:24131 370:24242 375:24362 380:24475 385:24580 390:24763 395:25006 400:25190 405:25308 410:25446 415:25555 420:25648 425:25761 430:25962 435:26057 440:26172 445:26260 450:26343 455:26414 460:26608 465:26720 470:26827 475:26979 480:27048 485:27126 490:27218 495:27272 500:27341 505:27433 510:27487 515:27535 520:27600 525:27758 530:27820 535:27896 540:27940 545:28085 550:28141 555:28298 560:28711 565:28732 570:28760 575:28792 580:28822 585:28995 590:29019 595:29059 600:29090 605:29119 610:29151 615:29182 620:29202 625:29238 630:29266 635:29294 640:29317 645:29472 650:29494 655:29599 660:29628 665:29781 670:29812 675:29868 680:29895 685:29923 690:29953 695:29973 700:30032 705:30048 710:30069 715:30089 720:30107 725:30128 730:30144 735:30168 740:30286 745:30312 750:30331 755:30369 760:30402 765:30420 770:30438 775:30584 780:30620 785:30647 790:30666 795:30682 800:30701 805:30712 810:30785 815:30801 820:30816 825:30831 830:30945 835:30979 840:31004 845:31102 850:31114 855:31132 860:31147 865:31166 870:31175 875:31205 880:31227 885:31253 890:31264 895:31280 900:31298 905:31314 910:31325 915:31337 920:31351 925:31370 930:31389 935:31405 940:31416 945:31442 950:31453 955:31470 960:31486 965:31680 970:31794 975:31803 980:31811 985:31836 990:32026 995:32126 1000:32142 \n-55:826 60:1707 65:2578 70:3373 75:4271 80:5020 85:5907 90:6893 95:7729 100:8434 105:9094 110:9712 115:10298 120:10911 125:11430 130:12005 135:12573 140:13234 145:13750 150:14314 155:14841 160:15333 165:15894 170:16323 175:16847 180:17319 185:17867 190:18337 195:18957 200:19402 205:19925 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710:39256 715:39279 720:39302 725:39334 730:39358 735:39388 740:39513 745:39537'..b'0:9632 155:9960 160:10258 165:10541 170:10816 175:11141 180:11384 185:11827 190:12048 195:12370 200:12608 205:12929 210:13142 215:13337 220:13642 225:13802 230:14032 235:14204 240:14349 245:14614 250:14773 255:14935 260:15217 265:15344 270:15512 275:15763 280:15966 285:16095 290:16255 295:16456 300:16589 305:16806 310:16956 315:17091 320:17476 325:17978 330:18165 335:18251 340:18393 345:18517 350:18606 355:18739 360:19210 365:19275 370:19358 375:19420 380:19510 385:19577 390:19668 395:19833 400:19955 405:20040 410:20154 415:20244 420:20323 425:20414 430:20577 435:20639 440:20724 445:20785 450:20835 455:20897 460:21073 465:21160 470:21235 475:21428 480:21486 485:21538 490:21599 495:21640 500:21685 505:21738 510:21773 515:21798 520:21863 525:22005 530:22044 535:22121 540:22162 545:22286 550:22340 555:22493 560:22814 565:22842 570:22869 575:22895 580:22927 585:23067 590:23090 595:23119 600:23134 605:23172 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175:12092 180:12358 185:12768 190:13022 195:13435 200:13746 205:14079 210:14229 215:14412 220:14688 225:14901 230:15155 235:15314 240:15475 245:15750 250:15938 255:16115 260:16396 265:16512 270:16704 275:16893 280:17127 285:17336 290:17484 295:17668 300:17788 305:18044 310:18177 315:18318 320:18785 325:19242 330:19399 335:19491 340:19646 345:19785 350:19886 355:19994 360:20481 365:20574 370:20675 375:20743 380:20827 385:20903 390:21012 395:21202 400:21349 405:21433 410:21527 415:21590 420:21649 425:21741 430:21888 435:21942 440:21998 445:22067 450:22121 455:22169 460:22293 465:22371 470:22476 475:22629 480:22666 485:22706 490:22765 495:22820 500:22881 505:22934 510:22988 515:23039 520:23087 525:23185 530:23226 535:23293 540:23332 545:23463 550:23513 555:23674 560:24058 565:24076 570:24095 575:24132 580:24156 585:24262 590:24278 595:24313 600:24336 605:24360 610:24396 615:24421 620:24459 625:24479 630:24498 635:24521 640:24542 645:24692 650:24712 655:24831 660:24853 665:24976 670:24991 675:25048 680:25063 685:25079 690:25095 695:25114 700:25163 705:25184 710:25202 715:25213 720:25227 725:25250 730:25276 735:25289 740:25384 745:25400 750:25416 755:25458 760:25483 765:25508 770:25530 775:25654 780:25671 785:25692 790:25715 795:25742 800:25752 805:25763 810:25832 815:25845 820:25862 825:25875 830:25890 835:25905 840:26020 845:26094 850:26108 855:26134 860:26150 865:26163 870:26174 875:26185 880:26200 885:26212 890:26225 895:26236 900:26250 905:26262 910:26279 915:26287 920:26299 925:26317 930:26325 935:26339 940:26356 945:26367 950:26381 955:26392 960:26404 965:26592 970:26701 975:26720 980:26743 985:26759 990:26969 995:26990 \n-\n-\n-null device \n- 1 \n-Creating the sampleMetadata file...\n-Creating TIC pdf...\n-Creating BIC pdf...\n-\n-\n-\tXSET OBJECT INFO\n-An "xcmsSet" object with 4 samples\n-\n-Time range: 0.7-1139.7 seconds (0-19 minutes)\n-Mass range: 50.0021-999.9863 m/z\n-Peaks: 59359 (about 14840 per sample)\n-Peak Groups: 0 \n-Sample classes: bio, blank \n-\n-Profile settings: method = bin\n- step = 0.01\n-\n-Memory usage: 6.02 MB\n-\n-\n-\tDONE\n' |
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| diff -r 0888f7ef739a -r 451ff602a957 test-data/sacuri_dir_root.zip |
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| Binary file test-data/sacuri_dir_root.zip has changed |