# HG changeset patch # User lecorguille # Date 1491565043 14400 # Node ID 27e7da5f6848fb1319b705c643ee7d96dd695c05 # Parent cb599006715f497e1ae97c8069cb72650aafad1b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 diff -r cb599006715f -r 27e7da5f6848 Makefile --- a/Makefile Mon Jan 30 08:54:06 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -# USAGE: make [install|clean] - -# -------- VARIABLE -------- - -OBJ=xcms_summary.tgz -DEP=abims_xcms_summary.xml xcms_summary.r tool_dependencies.xml repository_dependencies.xml test-data - - -# ------------------------ - -all: $(OBJ) - -$(OBJ): $(DEP) - tar --exclude=".svn" -zchf $@ $^ - -# ------------------------ - -install: $(OBJ) - mv *.tgz ~ - -clean: - rm *.tgz - diff -r cb599006715f -r 27e7da5f6848 README.rst --- a/README.rst Mon Jan 30 08:54:06 2017 -0500 +++ b/README.rst Fri Apr 07 07:37:23 2017 -0400 @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 1.0.3 - 03/02/2017** + +- IMPROVEMENT: xcms.summary can deal with merged individual data + **Version 1.0.2 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 @@ -16,12 +20,3 @@ - NEW: Create a summary of XCMS analysis -Test Status ------------ - -Planemo test using conda: failed - -Planemo test using source env.sh: passed - -Planemo shed_test : passed - diff -r cb599006715f -r 27e7da5f6848 abims_xcms_summary.xml --- a/abims_xcms_summary.xml Mon Jan 30 08:54:06 2017 -0500 +++ b/abims_xcms_summary.xml Fri Apr 07 07:37:23 2017 -0400 @@ -1,46 +1,50 @@ - - + + Create a summary of XCMS analysis macros.xml - + bioconductor-camera r-batch - + - + - + - + - + - + + + + + - + r-batch + + + bioconductor-xcms + + @@ -20,41 +25,101 @@ ; return=\$?; - mv log.txt $log; - cat $log; + mv log.txt '$log'; + cat '$log'; sh -c "exit \$return" - - #if $zipfile_load_conditional.zipfile_load_select == "yes": - #if $zipfile_load_conditional.zip_file: - zipfile $zipfile_load_conditional.zip_file + + #if $file_load_section.file_load_conditional.file_load_select == "yes": + #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #else + zipfile '$file_load_section.file_load_conditional.input' #end if #end if - - - - - - - + +
+ + + + + + + + + + + +
+ + + +
+ + + + +
+ + + +
+ + + + +
+ + + + #if $peaklist.peaklistBool + variableMetadataOutput '$variableMetadata' + dataMatrixOutput '$dataMatrix' + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + #end if + + + + + + + + + + + + + + - - - + - + + + (peaklist['peaklistBool']) + + + (peaklist['peaklistBool']) + + .. class:: infomark -**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu .. class:: infomark diff -r cb599006715f -r 27e7da5f6848 planemo_test.sh --- a/planemo_test.sh Mon Jan 30 08:54:06 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -# 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 - -#All 1 test(s) executed passed. -#abims_xcms_summary[0]: 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 1 test(s) executed passed. -#abims_xcms_summary[0]: 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 - - diff -r cb599006715f -r 27e7da5f6848 static/images/xcms_summary_workflow.png Binary file static/images/xcms_summary_workflow.png has changed diff -r cb599006715f -r 27e7da5f6848 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData Binary file test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData has changed diff -r cb599006715f -r 27e7da5f6848 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Fri Apr 07 07:37:23 2017 -0400 @@ -0,0 +1,115 @@ + + + + +[W4M] XCMS analysis summary + + + +

___ XCMS analysis summary using Workflow4Metabolomics ___

+
+

Samples used:

+
+ + +
samplefilenamemd5sum*
ko15 ./ko15.CDF 4698c36c0b3af007faf70975c04ccf2a
ko16 ./ko16.CDF afaeed94ced3140bc042d5ab6aeb16c1
wt15 ./wt15.CDF d58a27fad7c04ddddb0359ddc2b7ba68
wt16 ./wt16.CDF 29654e9f8ad48c1fbe2a41b9ba578f6e
+
*The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process. +
+

Function launched:

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
timestamp***functionargumentvalue
170203-11:04:42xcmsSetnSlaves1
methodcentWave
ppm25
peakwidth2050
170203-11:05:21xcmsSetnSlaves1
methodcentWave
ppm25
peakwidth2050
170203-11:06:21xcmsSetnSlaves1
methodcentWave
ppm25
peakwidth2050
170203-11:06:59xcmsSetnSlaves1
methodcentWave
ppm25
peakwidth2050
170203-14:38:53groupmethoddensity
sleep0.001
minfrac0.3
bw5
mzwid0.01
max50
170203-14:51:16retcormethodpeakgroups
smoothloess
extra1
missing1
span0.2
familygaussian
plottypedeviation
170203-15:27:58groupmethoddensity
sleep0.001
minfrac0.3
bw5
mzwid0.01
max50
170203-15:44:50fillPeaksmethodchrom
convertRTMinuteFALSE
numDigitsMZ4
numDigitsRT1
intvalinto
+
***timestamp format: yymmdd-hh:mm:ss +
+

Informations about the xcmsSet object:

+
+An "xcmsSet" object with 4 samples
+
+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 
+
+Peak picking was performed on MS1.
+Profile settings: method = bin
+                  step = 0.1
+
+Memory usage: 4.25 MB
+
+

Citations:

+
    +
  • To cite the XCMS package in publications use: +
      +
    • Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)
      • +
    • Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)
      • +
    • H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)
      • +
    +
    • +
  • To cite the CAMERA package in publications use: +
      +
    • Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)
      • +
    +
    • +
  • To cite the Workflow4Metabolimics (W4M) project in publications use: +
      +
    • Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813
      • +
    +
    • +
+ + diff -r cb599006715f -r 27e7da5f6848 test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html Fri Apr 07 07:37:23 2017 -0400 @@ -0,0 +1,95 @@ + + + + +[W4M] XCMS analysis summary + + + +

___ XCMS analysis summary using Workflow4Metabolomics ___

+
+

Samples used:

+
+ + +
samplefilenamemd5sum*
ko15 faahKO_reduce/KO/ko15.CDF 4698c36c0b3af007faf70975c04ccf2a
ko16 faahKO_reduce/KO/ko16.CDF afaeed94ced3140bc042d5ab6aeb16c1
wt15 faahKO_reduce/WT/wt15.CDF d58a27fad7c04ddddb0359ddc2b7ba68
wt16 faahKO_reduce/WT/wt16.CDF 29654e9f8ad48c1fbe2a41b9ba578f6e
+
*The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process. +
+

Function launched:

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
timestamp***functionargumentvalue
160420-14:09:46xcmsSetnSlaves1
methodcentWave
ppm25
peakwidth2050
160420-15:07:14groupmethoddensity
sleep0.001
minfrac0.3
bw5
mzwid0.01
max50
160421-11:10:32retcormethodpeakgroups
smoothloess
extra1
missing1
span0.2
familygaussian
plottypedeviation
160421-11:19:31groupmethoddensity
sleep0.001
minfrac0.3
bw5
mzwid0.01
max50
160421-11:50:48fillPeaksmethodchrom
+
***timestamp format: yymmdd-hh:mm:ss +
+

Informations about the xcmsSet object:

+
+An "xcmsSet" object with 4 samples
+
+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 = 0.1
+
+Memory usage: 4.25 MB
+
+

Citations:

+
    +
  • To cite the XCMS package in publications use: +
      +
    • Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)
      • +
    • Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)
      • +
    • H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)
      • +
    +
    • +
  • To cite the CAMERA package in publications use: +
      +
    • Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)
      • +
    +
    • +
  • To cite the Workflow4Metabolimics (W4M) project in publications use: +
      +
    • Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813
      • +
    +
    • +
+ + diff -r cb599006715f -r 27e7da5f6848 test-data/summary.html --- a/test-data/summary.html Mon Jan 30 08:54:06 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ - - - - -[W4M] XCMS analysis summary - - - -

___ XCMS analysis summary using Workflow4Metabolomics ___

-
-

Samples used:

-
- - -
samplefilenamemd5sum*
ko15 faahKO_reduce/KO/ko15.CDF 4698c36c0b3af007faf70975c04ccf2a
ko16 faahKO_reduce/KO/ko16.CDF afaeed94ced3140bc042d5ab6aeb16c1
wt15 faahKO_reduce/WT/wt15.CDF d58a27fad7c04ddddb0359ddc2b7ba68
wt16 faahKO_reduce/WT/wt16.CDF 29654e9f8ad48c1fbe2a41b9ba578f6e
-
*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. -
-

Function launched:

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
timestamp***functionargumentvalue
160420-14:09:46xcmsSetnSlaves1
methodcentWave
ppm25
peakwidth2050
160420-15:07:14groupmethoddensity
sleep0.001
minfrac0.3
bw5
mzwid0.01
max50
160421-11:10:32retcormethodpeakgroups
smoothloess
extra1
missing1
span0.2
familygaussian
plottypedeviation
160421-11:19:31groupmethoddensity
sleep0.001
minfrac0.3
bw5
mzwid0.01
max50
160421-11:50:48fillPeaksmethodchrom
-
***timestamp format: yymmdd-hh:mm:ss -
-

Informations about the xcmsSet object:

-
-An "xcmsSet" object with 4 samples
-
-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 = 0.1
-
-Memory usage: 4.25 MB
-
-

Citations:

-
    -
  • To cite the XCMS package in publications use: -
      -
    • Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)
      • -
    • Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)
      • -
    • H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)
      • -
    -
    • -
  • To cite the CAMERA package in publications use: -
      -
    • Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)
      • -
    -
    • -
  • To cite the Workflow4Metabolimics (W4M) project in publications use: -
      -
    • Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813
      • -
    -
    • -
- - diff -r cb599006715f -r 27e7da5f6848 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 30 08:54:06 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - - diff -r cb599006715f -r 27e7da5f6848 xcms_summary.r --- a/xcms_summary.r Mon Jan 30 08:54:06 2017 -0500 +++ b/xcms_summary.r Fri Apr 07 07:37:23 2017 -0400 @@ -6,7 +6,7 @@ # ----- ARGUMENTS BLACKLIST ----- #xcms.r -argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf") +argBlacklist=c("zipfile","singlefile_galaxyPath","singlefile_sampleName","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf") #CAMERA.r argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path") @@ -57,7 +57,7 @@ writehtml("") writehtml("[W4M] XCMS analysis summary") - + writehtml("