Mercurial > repos > lecorguille > xcms_xcmsset

changeset 7:451ff602a957 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author lecorguille
date Mon, 25 Apr 2016 11:14:02 -0400
parents 0888f7ef739a
children 53923784176c
files abims_xcms_xcmsSet.xml planemo_test.sh test-data/faahKO_reduce.zip test-data/sacuri_current_root.zip test-data/sacuri_dir_root.log.txt test-data/sacuri_dir_root.zip
diffstat 6 files changed, 43 insertions(+), 78 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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>
     
--- a/planemo_test.sh	Fri Apr 08 10:38:52 2016 -0400
+++ b/planemo_test.sh	Mon Apr 25 11:14:02 2016 -0400
@@ -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
+
Binary file test-data/faahKO_reduce.zip has changed
Binary file test-data/sacuri_current_root.zip has changed
--- 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
@@ -1,67 +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
-zipfile	/tmp/tmpAmhDSv/files/000/dataset_1.dat
-xfunction	xcmsSet
-xsetRdataOutput	/tmp/tmpAmhDSv/files/000/dataset_2.dat
-sampleMetadataOutput	/tmp/tmpAmhDSv/files/000/dataset_3.dat
-ticspdf	/tmp/tmpAmhDSv/files/000/dataset_4.dat
-bicspdf	/tmp/tmpAmhDSv/files/000/dataset_5.dat
-nSlaves	1
-method	matchedFilter
-step	0.01
-fwhm	4
-max	50
-snthresh	1
-steps	2
-
-
-	INFILE PROCESSING INFO
-
-
-	ARGUMENTS PROCESSING INFO
-files_root_directory	 sacuri 
-Compute md5 checksum...
-Checking XML structure...
-Checking files filenames compatibilities with xmcs...
-
-
-	MAIN PROCESSING INFO
-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 
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-55:514 60:1053 65:1583 70:2125 75:2648 80:3151 85:3818 90:4547 95:5274 100:5669 105:6164 110:6556 115:6922 120:7401 125:7782 130:8159 135:8514 140:9002 145:9296 150:9632 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 610:23197 615:23223 620:23242 625:23275 630:23304 635:23314 640:23339 645:23465 650:23490 655:23600 660:23619 665:23756 670:23781 675:23849 680:23870 685:23895 690:23910 695:23929 700:23992 705:24015 710:24026 715:24044 720:24068 725:24089 730:24122 735:24146 740:24242 745:24259 750:24280 755:24307 760:24330 765:24352 770:24373 775:24493 780:24514 785:24551 790:24563 795:24584 800:24605 805:24637 810:24684 815:24704 820:24715 825:24723 830:24736 835:24763 840:24854 845:24938 850:24950 855:24968 860:24983 865:25000 870:25019 875:25030 880:25046 885:25067 890:25084 895:25100 900:25119 905:25132 910:25141 915:25153 920:25170 925:25184 930:25199 935:25211 940:25224 945:25240 950:25251 955:25266 960:25278 965:25437 970:25548 975:25560 980:25568 985:25580 990:25784 995:25822 
-55:568 60:1154 65:1793 70:2433 75:3064 80:3635 85:4363 90:5039 95:5627 100:6077 105:6641 110:7124 115:7603 120:8076 125:8439 130:8836 135:9206 140:9628 145:9963 150:10288 155:10623 160:10937 165:11304 170:11676 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 
-
-
-null device 
-          1 
-Creating the sampleMetadata file...
-Creating TIC pdf...
-Creating BIC pdf...
-
-
-	XSET OBJECT INFO
-An "xcmsSet" object with 4 samples
-
-Time range: 0.7-1139.7 seconds (0-19 minutes)
-Mass range: 50.0021-999.9863 m/z
-Peaks: 59359 (about 14840 per sample)
-Peak Groups: 0 
-Sample classes: bio, blank 
-
-Profile settings: method = bin
-                  step = 0.01
-
-Memory usage: 6.02 MB
-
-
-	DONE
Binary file test-data/sacuri_dir_root.zip has changed