| Previous changeset 6:ca7c9a6da2c6 (2016-04-08) Next changeset 8:beb4446e6000 (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_summary.xml planemo_test.sh test-data/summary.html xcms_summary.r |
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added:
test-data/faahKO.xset.group.retcor.group.fillpeaks.RData |
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removed:
test-data/fillpeaks.RData |
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| diff -r ca7c9a6da2c6 -r ed8d80fc927c abims_xcms_summary.xml --- 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 |
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| @@ -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> |
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| diff -r ca7c9a6da2c6 -r ed8d80fc927c planemo_test.sh --- a/planemo_test.sh Fri Apr 08 10:40:12 2016 -0400 +++ b/planemo_test.sh Mon Apr 25 11:15:29 2016 -0400 |
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| @@ -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 + + |
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| diff -r ca7c9a6da2c6 -r ed8d80fc927c test-data/faahKO.xset.group.retcor.group.fillpeaks.RData |
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| Binary file test-data/faahKO.xset.group.retcor.group.fillpeaks.RData has changed |
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| diff -r ca7c9a6da2c6 -r ed8d80fc927c test-data/fillpeaks.RData |
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| Binary file test-data/fillpeaks.RData has changed |
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| diff -r ca7c9a6da2c6 -r ed8d80fc927c test-data/summary.html --- 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 |
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| @@ -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> |
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| diff -r ca7c9a6da2c6 -r ed8d80fc927c xcms_summary.r --- a/xcms_summary.r Fri Apr 08 10:40:12 2016 -0400 +++ b/xcms_summary.r Mon Apr 25 11:15:29 2016 -0400 |
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| @@ -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))) } |