Mercurial > repos > lecorguille > xcms_group

changeset 5:0306a96cc446 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author lecorguille
date Mon, 25 Apr 2016 11:14:27 -0400
parents 2db1d1d0f131
children 982d690f4e8c
files abims_xcms_group.xml planemo_test.sh test-data/faahKO.xset.RData test-data/faahKO.xset.group.retcor.RData test-data/xset.RData test-data/xset.group.retcor.RData test-data/xset.log.txt
diffstat 7 files changed, 54 insertions(+), 63 deletions(-) [+]
line wrap: on
line diff
--- a/abims_xcms_group.xml	Fri Apr 08 10:39:09 2016 -0400
+++ b/abims_xcms_group.xml	Mon Apr 25 11:14:27 2016 -0400
@@ -98,7 +98,7 @@
     </outputs>
 
     <tests>
-        <test>
+        <!--<test>
             <param name="image" value="xset.RData"/>
             <param name="methods|method" value="density"/>
             <param name="methods|bw" value="5"/>
@@ -116,8 +116,27 @@
                     <has_text text="Sample classes: bio, blank" />
                 </assert_contents>
             </output>
+        </test>-->
+        <test>
+            <param name="image" value="faahKO.xset.RData"/>
+            <param name="methods|method" value="density"/>
+            <param name="methods|bw" value="5"/>
+            <param name="methods|minfrac" value="0.3"/>
+            <param name="methods|mzwid" value="0.01"/>
+            <param name="methods|density_options|option" value="show"/>
+            <param name="methods|density_options|max" value="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: 8275" />
+                    <has_text text="Sample classes: KO, WT" />
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <!--<test>
             <param name="image" value="xset.group.retcor.RData"/>
             <param name="methods|method" value="density"/>
             <param name="methods|bw" value="5"/>
@@ -135,6 +154,25 @@
                     <has_text text="Sample classes: bio, blank" />
                 </assert_contents>
             </output>
+        </test>-->
+        <test>
+            <param name="image" value="faahKO.xset.group.retcor.RData"/>
+            <param name="methods|method" value="density"/>
+            <param name="methods|bw" value="5"/>
+            <param name="methods|minfrac" value="0.3"/>
+            <param name="methods|mzwid" value="0.01"/>
+            <param name="methods|density_options|option" value="show"/>
+            <param name="methods|density_options|max" value="50"/>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 4 samples" />
+                    <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 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: 8157" />
+                    <has_text text="Sample classes: KO, WT" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
--- a/planemo_test.sh	Fri Apr 08 10:39:09 2016 -0400
+++ b/planemo_test.sh	Mon Apr 25 11:14:27 2016 -0400
@@ -1,12 +1,8 @@
-planemo conda_init
-planemo conda_install .
-planemo test --install_galaxy --conda_dependency_resolution
-
-#All 2 test(s) executed passed.
-#abims_xcms_group[0]: passed
-#abims_xcms_group[1]: passed
+# Example of planemo command to launch test
 
 
+# -- 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
@@ -16,6 +12,17 @@
 #abims_xcms_group[1]: 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 2 test(s) executed passed.
+#abims_xcms_group[0]: passed
+#abims_xcms_group[1]: passed
+
+
+# -- Use of shed_test
 planemo shed_test --install_galaxy  -t testtoolshed
 
 #All 2 test(s) executed passed.
Binary file test-data/faahKO.xset.RData has changed
Binary file test-data/faahKO.xset.group.retcor.RData has changed
Binary file test-data/xset.RData has changed
Binary file test-data/xset.group.retcor.RData has changed
--- a/test-data/xset.log.txt	Fri Apr 08 10:39:09 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	group
-image	/tmp/tmp2L11lo/files/000/dataset_1.dat
-xsetRdataOutput	/tmp/tmp2L11lo/files/000/dataset_2.dat
-rplotspdf	/tmp/tmp2L11lo/files/000/dataset_3.dat
-method	density
-sleep	0.001
-minfrac	0.3
-bw	5
-mzwid	0.01
-max	50
-
-
-	INFILE PROCESSING INFO
-
-
-	ARGUMENTS PROCESSING INFO
-
-
-	MAIN PROCESSING INFO
-52 55 57 60 62 65 67 70 72 75 77 80 82 85 87 90 92 95 97 100 102 105 107 110 112 115 117 120 122 125 127 130 132 135 137 140 142 145 147 150 152 155 157 160 162 165 167 170 172 175 177 180 182 185 187 190 192 195 197 200 202 205 207 210 212 215 217 220 222 225 227 230 232 235 237 240 242 245 247 250 252 255 257 260 262 265 267 270 272 275 277 280 282 285 287 290 292 295 297 300 302 305 307 310 312 315 317 320 322 325 327 330 332 335 337 340 342 345 347 350 352 355 357 360 362 365 367 370 372 375 377 380 382 385 387 390 392 395 397 400 402 405 407 410 412 415 417 420 422 425 427 430 432 435 437 440 442 445 447 450 452 455 457 460 462 465 467 470 472 475 477 480 482 485 487 490 492 495 497 500 502 505 507 510 512 515 517 520 522 525 527 530 532 535 537 540 542 545 547 550 552 555 557 560 562 565 567 570 572 575 577 580 582 585 587 590 592 595 597 600 602 605 607 610 612 615 617 620 622 625 627 630 632 635 637 640 642 645 647 650 652 655 657 660 662 665 667 670 672 675 677 680 682 685 687 690 692 695 697 700 702 705 707 710 712 715 717 720 722 725 727 730 732 735 737 740 742 745 747 750 752 755 757 760 762 765 767 770 772 775 777 780 782 785 787 790 792 795 797 800 802 805 807 810 812 815 817 820 822 825 827 830 832 835 837 840 842 845 847 850 852 855 857 860 862 865 867 870 872 875 877 880 882 885 887 890 892 895 897 900 902 905 907 910 912 915 917 920 922 925 927 930 932 935 937 940 942 945 947 950 952 955 957 960 962 965 967 970 972 975 977 980 982 985 987 990 992 995 997 
-
-
-null device 
-          1 
-
-
-	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: 48998 
-Sample classes: bio, blank 
-
-Profile settings: method = bin
-                  step = 0.01
-
-Memory usage: 12 MB
-
-
-	DONE