| Next changeset 1:1592925c2e82 (2015-08-07) |
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Commit message:
planemo upload |
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added:
Makefile abims_xcms_xcmsSet.xml planemo.sh repository_dependencies.xml static/images/XCMS_Galaxy_workflow.png static/images/xcms_tics.png test-data/sacuri.zip test-data/sampleMetadata.tsv test-data/xset.BPCs_raw.pdf test-data/xset.RData test-data/xset.TICs_raw.pdf test-data/xset.log.txt tool_dependencies.xml xcms_set.tgz |
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| diff -r 000000000000 -r 054e4681667c Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Fri Aug 07 10:49:35 2015 -0400 |
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| @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=xcms_set.tgz +DEP=abims_xcms_xcmsSet.xml tool_dependencies.xml repository_dependencies.xml static test-data + + +# ------------------------ + +all: $(OBJ) + +$(OBJ): $(DEP) + tar --exclude=".svn" -zchf $@ $^ + +# ------------------------ + +install: $(OBJ) + mv *.tgz ~ + +clean: + rm *.tgz + |
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| diff -r 000000000000 -r 054e4681667c abims_xcms_xcmsSet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_xcmsSet.xml Fri Aug 07 10:49:35 2015 -0400 |
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| b'@@ -0,0 +1,403 @@\n+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2">\n+ \n+ <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>\n+ \n+ <requirements>\n+ <requirement type="package" version="3.1.2">R</requirement>\n+ <requirement type="binary">Rscript</requirement>\n+ <requirement type="package" version="1.44.0">xcms</requirement>\n+ <requirement type="package" version="2.1">xcms_w4m_script</requirement>\n+ </requirements>\n+ \n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+ \n+ <command>\n+ xcms.r\n+ #if $inputs.input == "lib":\n+ library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library\n+ #elif $inputs.input == "zip_file":\n+ zipfile $inputs.zip_file\n+ #end if\n+\n+ xfunction xcmsSet\n+ ## profmethod $profmethod \n+ nSlaves \\${GALAXY_SLOTS:-1} method $methods.method \n+ #if $methods.method == "centWave":\n+ ppm $methods.ppm\n+ peakwidth "c($methods.peakwidth)"\n+ #if $methods.options_scanrange.option == "show":\n+ scanrange "c($methods.options_scanrange.scanrange)"\n+ #end if \n+ #if $methods.options_c.option == "show":\n+ mzdiff $methods.options_c.mzdiff\n+ snthresh $methods.options_c.snthresh\n+ integrate $methods.options_c.integrate\n+ noise $methods.options_c.noise\n+ prefilter "c($methods.options_c.prefilter)"\n+ #end if\n+ #elif $methods.method == "matchedFilter":\n+ step $methods.step\n+ fwhm $methods.fwhm\n+ #if $methods.options_m.option == "show":\n+ ## sigma "$methods.options_m.sigma"\n+ max $methods.options_m.max\n+ snthresh $methods.options_m.snthresh\n+ ## mzdiff $methods.options_m.mzdiff\n+ steps $methods.options_m.steps\n+ ## sleep $methods.options_m.sleep\n+ #end if\n+ #elif $methods.method == "MSW":\n+ snthr $methods.snthr\n+ nearbyPeak $methods.nearbyPeak\n+ winSize.noise $methods.winSize_noise\n+ amp.Th $methods.amp_Th\n+ scales "c($methods.scales)"\n+ SNR.method "$methods.SNR_method"\n+ #end if\n+ && (mv xcmsSet.RData $xsetRData;\n+ mv sampleMetadata.tsv $sampleMetadata;\n+ mv TICs_raw.pdf $ticsRawPdf;\n+ mv BPCs_raw.pdf $bpcsRawPdf;\n+ mv xset.log $log);\n+ cat $log\n+ </command>\n+ \n+ <inputs>\n+\n+ <conditional name="inputs">\n+ <param name="input" type="select" label="Choose your inputs method" >\n+ <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>\n+ <option value="lib" >Library directory name</option>\n+ </param>\n+ <when value="zip_file">\n+ <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />\n+ </when>\n+ <when value="lib">\n+ <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >\n+ <validator type="empty_field"/> \n+ </param>\n+ </when>\n+\n+ </conditional>\n+\n+ \n+<!--\n+ <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >\n+ <option value="bin" selected="true">bin</option>\n+ <option value="binlin">binlin</option>\n+ <option value="binlinbase">binlinbase</option>\n+ <option value="intlin">intlin</option>\n+ </param>\n+ <param name="nSlaves" type="integer" value="9" label="MPI-slaves CPU'..b'.zip (containing all your conditions as sub-directories).\n+ | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.\n+\n+----------\n+Parameters\n+----------\n+\n+Extraction method for peaks detection\n+-------------------------------------\n+\n+**Matched Filter**\n+\n+ | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. \n+ | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).\n+\n+\n+**cent Wave**\n+\n+ | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.\n+ | Due to the fact that peak centroids are used, a binning step is not necessary.\n+ | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.\n+\n+**MSW**\n+\n+ | Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.\n+ | If you wish to have more details about the other parameters, you can read the following documents:\n+ | -Example of preprocessing data with XCMS : http://www.bioconductor.org/packages/2.12/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf\n+ | -Details and explanations for all the parameters of XCMS package: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf\n+\n+\n+------------\n+Output files\n+------------\n+\n+xset.TICs_raw.pdf\n+\n+ | "Total Ion Chromatograms" graph in pdf format.\n+\n+xset.BPCs_raw.pdf\n+\n+ | "Base Peak Chromatograms" graph in pdf format with each class samples opposed.\n+\n+sampleMetadata.tsv\n+\n+ | Tabular file that contains for each sample, it\'s associated class and polarity (positive,negative and mixed).\n+ | This file is necessary in the Anova and PCA step of the workflow.\n+\n+xset.RData: rdata.xcms.raw format\n+\n+ | Rdata file that is necessary in the second step of the workflow "xcms.group".\n+ \n+------\n+\n+.. class:: infomark \n+\n+The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.\n+\n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+Input files\n+-----------\n+\n+ | zip_file -> **sacuri.zip**\n+\n+Parameters\n+----------\n+\n+ | Method -> **matchedFilter**\n+ | step -> **0.01**\n+ | fwhm -> **4** \n+ | Advanced option -> **show**\n+ | max: -> **50**\n+ | snthresh -> **1**\n+ | steps -> **2**\n+\n+\n+Output files\n+------------\n+\n+ | **1) xset.RData: RData file**\n+\n+ | **2) Example of a sampleMetadata.tsv :**\n+\n+\n++---------------------------+------------+---------+\n+| sampleMetadata | class | polarity|\n++===========================+============+=========+\n+|HU_neg_017 | bio |negative |\n++---------------------------+------------+---------+\n+|HU_neg_028 | bio |negative |\n++---------------------------+------------+---------+\n+|HU_neg_034 | bio |negative |\n++---------------------------+------------+---------+\n+|Blanc04 | blank |negative |\n++---------------------------+------------+---------+\n+|Blanc06 | blank |negative |\n++---------------------------+------------+---------+\n+|Blanc09 | blank |negative |\n++---------------------------+------------+---------+\n+\n+\n+\n+ | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**\n+\n+.. image:: xcms_tics.png\n+\n+\n+ </help>\n+\n+\n+ <citations>\n+ <citation type="doi">10.1021/ac051437y</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ </citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 054e4681667c planemo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Fri Aug 07 10:49:35 2015 -0400 |
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| @@ -0,0 +1,1 @@ +planemo shed_init -f --name=xcms_xcms_set --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nFiltration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics" |
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| diff -r 000000000000 -r 054e4681667c repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Aug 07 10:49:35 2015 -0400 |
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| @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="12afb0ecb55f" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r 054e4681667c test-data/sacuri.zip |
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| diff -r 000000000000 -r 054e4681667c test-data/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tsv Fri Aug 07 10:49:35 2015 -0400 |
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| @@ -0,0 +1,10 @@ +sampleMetadata class polarity +HU_neg_028 bio negative +HU_neg_060 bio negative +HU_neg_051 bio negative +HU_neg_017 bio negative +HU_neg_034 bio negative +Blanc09 blank negative +Blanc06 blank negative +Blanc12 blank negative +Blanc04 blank negative |
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| diff -r 000000000000 -r 054e4681667c test-data/xset.BPCs_raw.pdf |
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| diff -r 000000000000 -r 054e4681667c test-data/xset.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xset.log.txt Fri Aug 07 10:49:35 2015 -0400 |
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| @@ -0,0 +1,56 @@ + PACKAGE INFO +parallel 3.1.1 +BiocGenerics 0.12.1 +Biobase 2.26.0 +Rcpp 0.11.5 +mzR 2.0.0 +igraph 0.7.1 +xcms 1.42.0 +snow 0.3.13 +batch 1.1.4 + + + ARGUMENTS INFO +zipfile /w/galaxy/galaxy4metabolomics/galaxy-dist/database/files/041/dataset_41794.dat +xfunction xcmsSet +nSlaves 8 +method matchedFilter +step 0.01 +fwhm 4 +max 50 +snthresh 1 +steps 2 + + + INFILE PROCESSING INFO + + + MAIN PROCESSING INFO +Starting snow cluster with 8 local sockets. +Detecting features in file # 1 : HU_neg_028.mzXML +Detecting features in file # 2 : HU_neg_060.mzXML +Detecting features in file # 3 : HU_neg_051.mzXML +Detecting features in file # 4 : HU_neg_017.mzXML +Detecting features in file # 5 : HU_neg_034.mzXML +Detecting features in file # 6 : Blanc09.mzXML +Detecting features in file # 7 : Blanc06.mzXML +Detecting features in file # 8 : Blanc12.mzXML +Detecting features in file # 9 : Blanc04.mzXML + + + XSET OBJECT INFO +An "xcmsSet" object with 9 samples + +Time range: 0.7-1140 seconds (0-19 minutes) +Mass range: 50.0019-999.9863 m/z +Peaks: 135846 (about 15094 per sample) +Peak Groups: 0 +Sample classes: bio, blank + +Profile settings: method = bin + step = 0.01 + +Memory usage: 13.8 MB + + + DONE |
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| diff -r 000000000000 -r 054e4681667c tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 07 10:49:35 2015 -0400 |
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| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="xcms" version="1.44.0"> + <repository changeset_revision="a1c3fc774157" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="xcms_w4m_script" version="2.1"> + <repository changeset_revision="c94c8ef520c8" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
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