Mercurial > repos > lecorguille > xcms_summary

changeset 7:ed8d80fc927c draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author lecorguille
date Mon, 25 Apr 2016 11:15:29 -0400
parents ca7c9a6da2c6
children beb4446e6000
files abims_xcms_summary.xml planemo_test.sh test-data/faahKO.xset.group.retcor.group.fillpeaks.RData test-data/fillpeaks.RData test-data/summary.html xcms_summary.r
diffstat 6 files changed, 56 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/abims_xcms_summary.xml	Fri Apr 08 10:40:12 2016 -0400
+++ b/abims_xcms_summary.xml	Mon Apr 25 11:15:29 2016 -0400
@@ -35,7 +35,7 @@
     
     <tests>
         <test>
-            <param name="image" value="fillpeaks.RData" />
+            <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" />
             <output name="htmlOutput" file="summary.html" />
         </test>
     </tests>
--- a/planemo_test.sh	Fri Apr 08 10:40:12 2016 -0400
+++ b/planemo_test.sh	Mon Apr 25 11:15:29 2016 -0400
@@ -1,10 +1,9 @@
-planemo conda_init
-planemo conda_install .
-#Linking packages ...
-#Error: ERROR: placeholder '/root/miniconda3/envs/_build_placehold_placehold_placehold_placehold_placehold_p' too short in: ncurses-5.9-4
+# 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-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh
 planemo test --install_galaxy
@@ -13,9 +12,19 @@
 #abims_xcms_summary[0]: passed
 
 
-planemo shed_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
+
+#All 1 test(s) executed passed.
+#abims_xcms_summary[0]: passed
 
-#All 2 test(s) executed passed.
-#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[0]: passed
-#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[1]: passed
+
+# -- Use of shed_test
+planemo shed_test --install_galaxy
 
+#All 1 test(s) executed passed.
+#toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/abims_xcms_summary/1.0.0[0]: passed
+
+
Binary file test-data/faahKO.xset.group.retcor.group.fillpeaks.RData has changed
Binary file test-data/fillpeaks.RData has changed
--- a/test-data/summary.html	Fri Apr 08 10:40:12 2016 -0400
+++ b/test-data/summary.html	Mon Apr 25 11:15:29 2016 -0400
@@ -16,44 +16,60 @@
 </div>
 <h2>Samples used:</h2>
 <div><table>
-<tr><th>sample</th><th>filename</th></tr>
-<tr> <td> HU_neg_051 </td> <td> sacuri//bio2/HU_neg_051.mzXML </td>  </tr><tr> <td> HU_neg_060 </td> <td> sacuri//bio2/HU_neg_060.mzXML </td>  </tr><tr> <td> HU_neg_017 </td> <td> sacuri//bio/HU_neg_017.mzXML </td>  </tr><tr> <td> HU_neg_028 </td> <td> sacuri//bio/HU_neg_028.mzXML </td>  </tr><tr> <td> Blanc04 </td> <td> sacuri//blank/Blanc04.mzXML </td>  </tr><tr> <td> Blanc06 </td> <td> sacuri//blank/Blanc06.mzXML </td>  </tr>
+<tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
+<tr> <td> ko15 </td> <td> faahKO_reduce/KO/ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> faahKO_reduce/KO/ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> faahKO_reduce/WT/wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> faahKO_reduce/WT/wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr>
 </table>
-
+<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.
 </div>
 <h2>Function launched:</h2>
 <div><table>
 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
-<tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td>
+<tr><td rowspan='4'>160420-14:09:46</td><td rowspan='4'>xcmsSet</td>
 <td>nSlaves</td><td>1</td></tr>
-<tr><td>method</td><td>matchedFilter</td></tr>
-<tr><td>step</td><td>0.01</td></tr>
-<tr><td>fwhm</td><td>30</td></tr>
-<tr><td rowspan='5'>151221-16:37:00</td><td rowspan='5'>group</td>
+<tr><td>method</td><td>centWave</td></tr>
+<tr><td>ppm</td><td>25</td></tr>
+<tr><td>peakwidth</td><td>2050</td></tr>
+<tr><td rowspan='6'>160420-15:07:14</td><td rowspan='6'>group</td>
 <td>method</td><td>density</td></tr>
 <tr><td>sleep</td><td>0.001</td></tr>
-<tr><td>minfrac</td><td>0.5</td></tr>
-<tr><td>bw</td><td>30</td></tr>
-<tr><td>mzwid</td><td>0.25</td></tr>
-<tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td>
+<tr><td>minfrac</td><td>0.3</td></tr>
+<tr><td>bw</td><td>5</td></tr>
+<tr><td>mzwid</td><td>0.01</td></tr>
+<tr><td>max</td><td>50</td></tr>
+<tr><td rowspan='7'>160421-11:10:32</td><td rowspan='7'>retcor</td>
+<td>method</td><td>peakgroups</td></tr>
+<tr><td>smooth</td><td>loess</td></tr>
+<tr><td>extra</td><td>1</td></tr>
+<tr><td>missing</td><td>1</td></tr>
+<tr><td>span</td><td>0.2</td></tr>
+<tr><td>family</td><td>gaussian</td></tr>
+<tr><td>plottype</td><td>deviation</td></tr>
+<tr><td rowspan='6'>160421-11:19:31</td><td rowspan='6'>group</td>
+<td>method</td><td>density</td></tr>
+<tr><td>sleep</td><td>0.001</td></tr>
+<tr><td>minfrac</td><td>0.3</td></tr>
+<tr><td>bw</td><td>5</td></tr>
+<tr><td>mzwid</td><td>0.01</td></tr>
+<tr><td>max</td><td>50</td></tr>
+<tr><td rowspan='1'>160421-11:50:48</td><td rowspan='1'>fillPeaks</td>
 <td>method</td><td>chrom</td></tr>
 </table>
 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss
 </div>
 <h2>Informations about the xcmsSet object:</h2>
 <div><pre>
-An "xcmsSet" object with 6 samples
+An "xcmsSet" object with 4 samples
 
-Time range: 16.3-1138.9 seconds (0.3-19 minutes)
-Mass range: 61.9883-481.2446 m/z
-Peaks: 1799 (about 300 per sample)
-Peak Groups: 289 
-Sample classes: bio, bio2, blank 
+Time range: 2506-4484 seconds (41.8-74.7 minutes)
+Mass range: 200.1-600 m/z
+Peaks: 32720 (about 8180 per sample)
+Peak Groups: 8157 
+Sample classes: KO, WT 
 
 Profile settings: method = bin
-                  step = 0.01
+                  step = 0.1
 
-Memory usage: 0.421 MB
+Memory usage: 4.25 MB
 </pre></div>
 <h2>Citations:</h2>
 <div><ul>
--- a/xcms_summary.r	Fri Apr 08 10:40:12 2016 -0400
+++ b/xcms_summary.r	Mon Apr 25 11:15:29 2016 -0400
@@ -12,8 +12,9 @@
 
 # ----- PACKAGE -----
 
-pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "tcltk","igraph", "xcms","snow","CAMERA","multtest","batch")
+pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","CAMERA","batch")
 for(pkg in pkgs) {
+    cat(pkg,"\n")
     suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
 }