| Next changeset 1:4753e64cf694 (2017-05-03) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty |
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LICENSE.md README.md build.xml profia_config.xml profia_wrapper.R runit/output/dataMatrix.tsv runit/output/figure.pdf runit/output/information.txt runit/output/sampleMetadata.tsv runit/output/variableMetadata.tsv runit/plasFIA/C100a.mzML runit/plasFIA/C100b.mzML runit/plasFIA/C100c.mzML runit/plasfia/plasFIA.zip runit/profia_runtests.R runit/profia_tests.R static/images/profia_workflowPositionImage.png static/images/profia_workingExampleImage.png test-data/input-plasFIA.zip test-data/output-dataMatrix.tsv test/test-profia |
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| diff -r 000000000000 -r 39ccace77270 LICENSE.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE.md Sun Mar 26 17:37:12 2017 -0400 |
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| b'@@ -0,0 +1,517 @@\n+ CeCILL FREE SOFTWARE LICENSE AGREEMENT\n+\n+Version 2.1 dated 2013-06-21\n+\n+\n+ Notice\n+\n+This Agreement is a Free Software license agreement that is the result\n+of discussions between its authors in order to ensure compliance with\n+the two main principles guiding its drafting:\n+\n+ * firstly, compliance with the principles governing the distribution\n+ of Free Software: access to source code, broad rights granted to users,\n+ * secondly, the election of a governing law, French law, with which it\n+ is conformant, both as regards the law of torts and intellectual\n+ property law, and the protection that it offers to both authors and\n+ holders of the economic rights over software.\n+\n+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) \n+license are: \n+\n+Commissariat \xe0 l\'\xe9nergie atomique et aux \xe9nergies alternatives - CEA, a\n+public scientific, technical and industrial research establishment,\n+having its principal place of business at 25 rue Leblanc, immeuble Le\n+Ponant D, 75015 Paris, France.\n+\n+Centre National de la Recherche Scientifique - CNRS, a public scientific\n+and technological establishment, having its principal place of business\n+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.\n+\n+Institut National de Recherche en Informatique et en Automatique -\n+Inria, a public scientific and technological establishment, having its\n+principal place of business at Domaine de Voluceau, Rocquencourt, BP\n+105, 78153 Le Chesnay cedex, France.\n+\n+\n+ Preamble\n+\n+The purpose of this Free Software license agreement is to grant users\n+the right to modify and redistribute the software governed by this\n+license within the framework of an open source distribution model.\n+\n+The exercising of this right is conditional upon certain obligations for\n+users so as to preserve this status for all subsequent redistributions.\n+\n+In consideration of access to the source code and the rights to copy,\n+modify and redistribute granted by the license, users are provided only\n+with a limited warranty and the software\'s author, the holder of the\n+economic rights, and the successive licensors only have limited liability.\n+\n+In this respect, the risks associated with loading, using, modifying\n+and/or developing or reproducing the software by the user are brought to\n+the user\'s attention, given its Free Software status, which may make it\n+complicated to use, with the result that its use is reserved for\n+developers and experienced professionals having in-depth computer\n+knowledge. Users are therefore encouraged to load and test the\n+suitability of the software as regards their requirements in conditions\n+enabling the security of their systems and/or data to be ensured and,\n+more generally, to use and operate it in the same conditions of\n+security. This Agreement may be freely reproduced and published,\n+provided it is not altered, and that no provisions are either added or\n+removed herefrom.\n+\n+This Agreement may apply to any or all software for which the holder of\n+the economic rights decides to submit the use thereof to its provisions.\n+\n+Frequently asked questions can be found on the official website of the\n+CeCILL licenses family (http://www.cecill.info/index.en.html) for any \n+necessary clarification.\n+\n+\n+ Article 1 - DEFINITIONS\n+\n+For the purpose of this Agreement, when the following expressions\n+commence with a capital letter, they shall have the following meaning:\n+\n+Agreement: means this license agreement, and its possible subsequent\n+versions and annexes.\n+\n+Software: means the software in its Object Code and/or Source Code form\n+and, where applicable, its documentation, "as is" when the Licensee\n+accepts the Agreement.\n+\n+Initial Software: means the Software in its Source Code and possibly its\n+Object Code form and, where applicable, its documentation, "as is" when\n+it is first distributed under the terms and conditions of the Agreement.\n+\n+Modified Software: means the Software modified by at lea'..b"l be\n+decided on a case-by-case basis between the relevant Licensor and the\n+Licensee pursuant to a memorandum of understanding. The Licensor\n+disclaims any and all liability as regards the Licensee's use of the\n+name of the Software. No warranty is given as regards the existence of\n+prior rights over the name of the Software or as regards the existence\n+of a trademark.\n+\n+\n+ Article 10 - TERMINATION\n+\n+10.1 In the event of a breach by the Licensee of its obligations\n+hereunder, the Licensor may automatically terminate this Agreement\n+thirty (30) days after notice has been sent to the Licensee and has\n+remained ineffective.\n+\n+10.2 A Licensee whose Agreement is terminated shall no longer be\n+authorized to use, modify or distribute the Software. However, any\n+licenses that it may have granted prior to termination of the Agreement\n+shall remain valid subject to their having been granted in compliance\n+with the terms and conditions hereof.\n+\n+\n+ Article 11 - MISCELLANEOUS\n+\n+\n+ 11.1 EXCUSABLE EVENTS\n+\n+Neither Party shall be liable for any or all delay, or failure to\n+perform the Agreement, that may be attributable to an event of force\n+majeure, an act of God or an outside cause, such as defective\n+functioning or interruptions of the electricity or telecommunications\n+networks, network paralysis following a virus attack, intervention by\n+government authorities, natural disasters, water damage, earthquakes,\n+fire, explosions, strikes and labor unrest, war, etc.\n+\n+11.2 Any failure by either Party, on one or more occasions, to invoke\n+one or more of the provisions hereof, shall under no circumstances be\n+interpreted as being a waiver by the interested Party of its right to\n+invoke said provision(s) subsequently.\n+\n+11.3 The Agreement cancels and replaces any or all previous agreements,\n+whether written or oral, between the Parties and having the same\n+purpose, and constitutes the entirety of the agreement between said\n+Parties concerning said purpose. No supplement or modification to the\n+terms and conditions hereof shall be effective as between the Parties\n+unless it is made in writing and signed by their duly authorized\n+representatives.\n+\n+11.4 In the event that one or more of the provisions hereof were to\n+conflict with a current or future applicable act or legislative text,\n+said act or legislative text shall prevail, and the Parties shall make\n+the necessary amendments so as to comply with said act or legislative\n+text. All other provisions shall remain effective. Similarly, invalidity\n+of a provision of the Agreement, for any reason whatsoever, shall not\n+cause the Agreement as a whole to be invalid.\n+\n+\n+ 11.5 LANGUAGE\n+\n+The Agreement is drafted in both French and English and both versions\n+are deemed authentic.\n+\n+\n+ Article 12 - NEW VERSIONS OF THE AGREEMENT\n+\n+12.1 Any person is authorized to duplicate and distribute copies of this\n+Agreement.\n+\n+12.2 So as to ensure coherence, the wording of this Agreement is\n+protected and may only be modified by the authors of the License, who\n+reserve the right to periodically publish updates or new versions of the\n+Agreement, each with a separate number. These subsequent versions may\n+address new issues encountered by Free Software.\n+\n+12.3 Any Software distributed under a given version of the Agreement may\n+only be subsequently distributed under the same version of the Agreement\n+or a subsequent version, subject to the provisions of Article 5.3.4\n+<#compatibility>.\n+\n+\n+ Article 13 - GOVERNING LAW AND JURISDICTION\n+\n+13.1 The Agreement is governed by French law. The Parties agree to\n+endeavor to seek an amicable solution to any disagreements or disputes\n+that may arise during the performance of the Agreement.\n+\n+13.2 Failing an amicable solution within two (2) months as from their\n+occurrence, and unless emergency proceedings are necessary, the\n+disagreements or disputes shall be referred to the Paris Courts having\n+jurisdiction, by the more diligent Party.\n" |
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| diff -r 000000000000 -r 39ccace77270 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sun Mar 26 17:37:12 2017 -0400 |
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| @@ -0,0 +1,62 @@ +Preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry data (FIA-HRMS) +=============================================================================================================== + +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure + +Status: [](https://travis-ci.org/workflow4metabolomics/profia). + +### Description + +**Version:** 3.0.0 +**Date:** 2017-03-21 +**Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) +**Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) +**Citation:** Delabriere A., Hohenester U., Junot C. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. +**Licence:** CeCILL +**Reference history:** +**Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) + +### Installation + +* Configuration file: `profia_config.xml` +* Image files: + + `static/images/profia_workflowPositionImage.png` + + `static/images/profia_workingExampleImage.png` +* Wrapper file: `profia_wrapper.R` +* R packages + + **batch** from CRAN + + ```r + install.packages("batch", dep=TRUE) + install.packages("FNN", dep=TRUE) + install.packages("maxLik", dep=TRUE) + install.packages("minpack.lm", dep=TRUE) + install.packages("pracma", dep=TRUE) + ``` + + **profia** from Bioconductor + + ```r + source("http://www.bioconductor.org/biocLite.R") + biocLite("xcms") + biocLite("proFIA") + biocLite("plasFIA") + ``` + +### Tests + +The code in the wrapper can be tested by running the `runit/profia_runtests.R` R file + +You will need to install **RUnit** package in order to make it run: +```r +install.packages('RUnit', dependencies = TRUE) +``` + +### Working example + +### News + +###### CHANGES IN VERSION 3.0.0 + +NEW FEATURE + + * Creation of the tool |
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| diff -r 000000000000 -r 39ccace77270 build.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build.xml Sun Mar 26 17:37:12 2017 -0400 |
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| @@ -0,0 +1,87 @@ +<project name="w4m.profia" default="all"> + + <property name="tool.xml" value="profia_config.xml"/> + <property name="conda.dir" value="${user.home}/w4m-conda"/> + + <!--~~~ + ~ ALL ~ + ~~~~~--> + + <target name="all"/> + + <!--~~~~ + ~ TEST ~ + ~~~~~--> + + <target name="test" depends="plain.test,planemo.lint,planemo.test"/> + + <!--~~~~~~~~~~ + ~ PLAIN TEST ~ + ~~~~~~~~~~~--> + + <target name="plain.test"> + <exec executable="test/test-profia" failonerror="true"/> + </target> + + <!--~~~~~~~~~~~~ + ~ PLANEMO LINT ~ + ~~~~~~~~~~~~~--> + + <target name="planemo.lint"> + <exec executable="planemo" failonerror="true"> + <arg value="lint"/> + <arg value="${tool.xml}"/> + </exec> + </target> + + <!--~~~~~~~~~~~~ + ~ PLANEMO TEST ~ + ~~~~~~~~~~~~~--> + + <target name="planemo.test" depends="planemo.conda.install"> + <exec executable="planemo" failonerror="true"> + <arg value="test"/> + <arg value="--conda_prefix"/> + <arg value="${conda.dir}"/> + <arg value="--galaxy_branch"/> + <arg value="release_16.07"/> + <arg value="--conda_dependency_resolution"/> + <arg value="${tool.xml}"/> + </exec> + </target> + + <!--~~~~~~~~~~~~~~~~~~~~~ + ~ PLANEMO CONDA INSTALL ~ + ~~~~~~~~~~~~~~~~~~~~~~--> + + <target name="planemo.conda.install" depends="planemo.conda.init"> + <exec executable="planemo" failonerror="true"> + <arg value="conda_install"/> + <arg value="--conda_prefix"/> + <arg value="${conda.dir}"/> + <arg value="${tool.xml}"/> + </exec> + </target> + + <!--~~~~~~~~~~~~~~~~~~ + ~ PLANEMO CONDA INIT ~ + ~~~~~~~~~~~~~~~~~~~--> + + <available file="${conda.dir}" property="conda.is.installed"/> + <target name="planemo.conda.init" unless="conda.is.installed"> + <exec executable="planemo" failonerror="true"> + <arg value="conda_init"/> + <arg value="--conda_prefix"/> + <arg value="${conda.dir}"/> + </exec> + </target> + + <!--~~~~~ + ~ CLEAN ~ + ~~~~~~--> + + <target name="clean"> + <delete dir="${conda.dir}"/> + </target> + +</project> |
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| diff -r 000000000000 -r 39ccace77270 profia_config.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profia_config.xml Sun Mar 26 17:37:12 2017 -0400 |
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| b'@@ -0,0 +1,283 @@\n+<tool id="profia" name="proFIA" version="3.0.0">\n+ <description>Preprocessing of FIA-HRMS data</description>\n+ \n+ <requirements>\n+ <requirement type="package">r-batch</requirement>\n+ <requirement type="package">r-FNN</requirement>\n+ <requirement type="package">r-maxLik</requirement>\n+ <requirement type="package">r-minpack.lm</requirement>\n+ <requirement type="package">r-pracma</requirement>\n+ <requirement type="package">bioconductor-proFIA</requirement>\n+ </requirements>\n+ \n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+ \n+ <command><![CDATA[\n+ Rscript $__tool_directory__/profia_wrapper.R\n+\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 $inputs.zip_file\n+ #end if\n+ \n+ ppmN "$ppmN"\n+ ppmGroupN "$ppmGroupN"\n+ fracGroupN "$fracGroupN"\n+ kI "$kI"\n+\n+ dataMatrix_out "$dataMatrix_out"\n+ sampleMetadata_out "$sampleMetadata_out"\n+ variableMetadata_out "$variableMetadata_out"\n+ figure "$figure"\n+ information "$information"\n+ ]]></command>\n+ \n+ <inputs>\n+ <conditional name="inputs">\n+ <param name="input" type="select" label="Choose your input method" >\n+ <option value="zip_file" selected="true">Zip file from your history containing your raw files</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,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+ </conditional>\n+ \n+ <param name="ppmN" label="Maximum deviation between centroids during band detection (in ppm)" type="text" value = "5" help="[ppm]" />\t \n+ <param name="ppmGroupN" label="Accuracy of the mass spectrometer to be used during feature alignment (in ppm)" type="text" value = "5" help="[ppmGroup] Should be inferior or equal to the deviation parameter above." />\n+ <param name="fracGroupN" label=" Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment" type="text" value = "0.5" help="[fracGroup]" />\n+ <param name="kI" label="Number of neighbour features to be used for imputation (select 0 to skip the imputation step)" type="text" value = "5" help="[k]" />\n+ </inputs>\n+ \n+ <outputs>\n+ <data name="dataMatrix_out" label="${tool.name}_dataMatrix.tsv" format="tabular" ></data>\n+ <data name="sampleMetadata_out" label="${tool.name}_sampleMetadata.tsv" format="tabular" ></data>\n+ <data name="variableMetadata_out" label="${tool.name}_variableMetadata.tsv" format="tabular" ></data>\n+ <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/>\n+ <data name="information" label="${tool.name}_information.txt" format="txt"/>\n+ </outputs>\n+ \n+ <tests>\n+ <test>\n+ <param name="inputs|input" value="zip_file" />\n+ <param name="inputs|zip_file" value="input-plasFIA.zip" ftype="zip" />\n+ <param name="ppmN" value="2"/>\n+ <param name="ppmGroupN" value="1"/>\n+ <param name="fracGroupN" value="0.1"/>\n+ <param name="kI" value="2"/>\n+ <output name="dataMatrix_out" file="output-dataMatrix.tsv"/>\n+ </test>\n+ </tests>\n+ \n+ <help>\t\n+\n+.. class:: infomark\n+\n+**Author**\tAlexis Delabriere and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr)\n+\n+---------------------------------------------------\n+\n+.. class:: infomark\n+\n+**Please cite**\n+\n+Delabriere A., Hohenester U., Junot C. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.\n+\n+-----------------------------------------------'..b' **All Levels (1-)** : Centroid Mode\n+Use zlib: **64**\n+Binary Encoding: **64**\n+m/z Encoding: **64**\n+Intensity Encoding: **64**\n+\n+----------\n+Parameters\n+----------\n+ \n+Maximum deviation between centroids during band detection; in ppm (default = 5)\n+\t| m/z tolerance of centroids corresponding to the same ion from one scan to the other.\n+\t| \n+\n+Accuracy of the mass spectrometer to be used during feature alignment; in ppm (default = 5)\n+\t| Should be inferior or equal to the deviation parameter above.\n+\t| \n+ \n+Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment (default = 0.5)\n+\t| Identical to the corresponding parameter in XCMS. \n+\t| \n+\n+Number of neighbour features to be used for imputation (default = 5)\n+\t| Select 0 to skip the imputation step. \n+\t| \t\n+\n+\n+------------\n+Output files\n+------------\n+\n+dataMatrix.tabular\n+\t| **dataMatrix** tabular separated file with the variables as rows and samples as columns. Missing values are indicated as \'NA\' (i.e. when the signal was not significantly different from noise).\n+\t|\n+\t\n+sampleMetadata.tabular\n+\t| **sampleMetadata** tabular separated file containing the sample metadata as columns.\n+\t| \n+\t\n+variableMetadata.tabular\n+\t| **variableMetadata** tabular separated file containing the variable metadata as columns. The **timeShifted** flag is set to 1 when the flowgram is time shifted compared to the sample peak (probably due to liquid retention in the FI tube). The **corSampPeakMean** metric is the correlation between the feature flowgram and the sample peak (values are in [-1, 1]). A value below 0.2 suggests that the feature signal is affected by a strong matrix effect. The **meanSolvent** is the mean baseline signal in the feature flowgrams. The **signalOverSolventPvalueMean** is the mean p-value of the tests discriminating between signal and baseline solvent.\n+\t| \n+\n+figure.pdf\n+\t| Visualization and diagnostics about the preprocessed data set; **Feature quality**: Number of detected features per sample for each of the three categories: \'Well-behaved\' features have a peak shape close to the sample peak (optimal FIA acquisition is achieved when the majority of the features fall into this category); \'Shifted\' indicates a time shift compared to the sample peak, and probably results from retention in the FI tube; \'Significant Matrix Effect\' corresponds to a correlation between the feature and the samples peaks of less than 0.2, which is usually caused by a strong matrix effect; **Sample peaks**: Visualization of the peak model for each sample; should have close shapes in case of similar FIA conditions; **m/z density**: may allow to detect a missing m/z value, and in turn, suggest that the *ppm* parameter should be modified; **PCA score plot** of the log10 intensities to detect sample outliers.\n+\t| \n+\t\t\t\n+information.txt\n+\t| Text file with all messages and warnings generated during the computation.\n+\t|\n+\n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+Figure output\n+=============\n+\n+.. image:: profia_workingExampleImage.png\n+ :width: 600\n+ \n+---------------------------------------------------\n+\n+----\n+NEWS\n+----\n+\n+CHANGES IN VERSION 3.0.0\n+========================\n+\n+NEW FEATURE\n+\n+Creation of the tool\n+\n+</help>\n+\n+<citations>\n+ <citation type="bibtex">@Article{DelabriereSubmitted,\n+ Title = {proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry},\n+ Author = {Delabriere, Alexis and Hohenester, Ulli and Junot, Christophe and Thevenot, Etienne A},\n+ Journal = {submitted},\n+ Year = {submitted},\n+ Pages = {--},\n+ Volume = {},\n+ Doi = {}\n+ }</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+</citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 39ccace77270 profia_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profia_wrapper.R Sun Mar 26 17:37:12 2017 -0400 |
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| @@ -0,0 +1,210 @@ +#!/usr/bin/env Rscript + +library(batch) ## parseCommandArgs + +argVc <- unlist(parseCommandArgs(evaluate=FALSE)) + +##------------------------------ +## Initializing +##------------------------------ + + +## libraries +##---------- + +suppressMessages(library(proFIA)) + + +## constants +##---------- + +modNamC <- "proFIA" ## module name + + +## log file +##--------- + +sink(argVc["information"]) + +cat("\nStart of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + + +## arguments +##---------- + + +if("zipfile" %in% names(argVc)) { + + zipfile <- argVc["zipfile"] + + ## We unzip automatically the raw files from the zip file + + if(exists("zipfile") && (zipfile!="")) { + if(!file.exists(zipfile)){ + error_message=paste("Cannot access the Zip file:", zipfile) + print(error_message) + stop(error_message) + } + + ## unzip + + suppressWarnings(unzip(zipfile, unzip="unzip")) + + ## get the directory name + + filesInZip=unzip(zipfile, list=T); + directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); + directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] + directory = "." + if (length(directories) == 1) directory = directories + + cat("files_root_directory\t",directory,"\n") + + } + +} else if ("library" %in% names(argVc)) { + + directory <- argVc["library"] + + if(!file.exists(directory)) { + + error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.") + print(error_message) + stop(error_message) + + } + +} else { + + error_message <- "No zipfile nor input library available" + print(error_message) + stop(error_message) + +} + +##------------------------------ +## Computations +##------------------------------ + + +optWrnN <- options()$warn +options(warn = -1) + +stpI <- 1 + +cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "") + +fiaset <- proFIAset(directory, + ppm = as.numeric(argVc["ppmN"]), + parallel = FALSE) + +stpI <- stpI + 1 + +cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "") + +fiaset <- group.FIA(fiaset, + ppmGroup = as.numeric(argVc["ppmGroupN"]), + fracGroup = as.numeric(argVc["fracGroupN"])) + +stpI <- stpI + 1 + +cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "") + +fiaset <- makeDataMatrix(fiaset, + maxo = FALSE) + +stpI <- stpI + 1 + +kI <- as.integer(argVc["kI"]) + +if(kI > 0) { + + cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "") + + fiaset <- imputeMissingValues.WKNN_TN(fiaset, + k = kI) + + stpI <- stpI + 1 +} + +options(warn = optWrnN) + + +##------------------------------ +## Ending +##------------------------------ + + +## Plotting +##--------- + +cat("\n", stpI, ") Plotting ('plot'):\n", sep = "") + +pdf(argVc["figure"]) + +plot(fiaset) + +dev.off() + +stpI <- stpI + 1 + +## Printing +##--------- + +cat("\n", stpI, ") Printing ('show'):\n", sep = "") + +fiaset + +stpI <- stpI + 1 + +## Exporting +##---------- + +cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "") + +datMN <- exportDataMatrix(fiaset) +samDF <- exportSampleMetadata(fiaset) +varDF <- exportVariableMetadata(fiaset) + +if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) { + datDF <- as.data.frame(t(datMN)) +} else { + datDF <- as.data.frame(datMN) +} +rownames(varDF) <- rownames(datDF) + +datDF <- cbind.data.frame(dataMatrix = rownames(datDF), + datDF) +write.table(datDF, + file = argVc["dataMatrix_out"], + quote = FALSE, + row.names = FALSE, + sep = "\t") + +samDF <- cbind.data.frame(sampleMetadata = rownames(samDF), + samDF) +write.table(samDF, + file = argVc["sampleMetadata_out"], + quote = FALSE, + row.names = FALSE, + sep = "\t") + +varDF <- cbind.data.frame(variableMetadata = rownames(varDF), + varDF) +write.table(varDF, + file = argVc["variableMetadata_out"], + quote = FALSE, + row.names = FALSE, + sep = "\t") + + +## Closing +##-------- + +cat("\nEnd of '", modNamC, "' Galaxy module call: ", + as.character(Sys.time()), "\n", sep = "") + +sink() + +rm(list = ls()) |
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| diff -r 000000000000 -r 39ccace77270 runit/output/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/dataMatrix.tsv Sun Mar 26 17:37:12 2017 -0400 |
| b |
| b'@@ -0,0 +1,720 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|
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| diff -r 000000000000 -r 39ccace77270 runit/output/figure.pdf |
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| Binary file runit/output/figure.pdf has changed |
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| diff -r 000000000000 -r 39ccace77270 runit/output/information.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/information.txt Sun Mar 26 17:37:12 2017 -0400 |
| b |
| @@ -0,0 +1,35 @@ + +Start of the 'proFIA' Galaxy module call: Sat 25 Mar 2017 08:55:32 PM +files_root_directory plasFIA + +1) Peak detection step ('proFIAset'): + +2) Peak alignment ('group.FIA'): + + 719 groups have been done . + +3) Creating the peak table ('makeDataMatrix'): + +4) Imputing missing values ('imputeMissingValues.WKNN_TN'): + +5) Plotting ('plot'): +PCA +3 samples x 648 variables +standard scaling of predictors +71 excluded variables (near zero variance) + R2X(cum) pre ort +Total 1 2 0 +null device + 1 + +6) Printing ('show'): +A "proFIAset" object containing 1 classes. +Missing values have been imputed. +2161 peaks detected. +719 features have been grouped. +The data matrix is avalaible. +Memory usage: 0.425 MB + +7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'): + +End of 'proFIA' Galaxy module call: 2017-03-25 21:22:13 |
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| diff -r 000000000000 -r 39ccace77270 runit/output/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/sampleMetadata.tsv Sun Mar 26 17:37:12 2017 -0400 |
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| @@ -0,0 +1,4 @@ +sampleMetadata sampleID class +1 C100a plasFIA +2 C100b plasFIA +3 C100c plasFIA |
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| diff -r 000000000000 -r 39ccace77270 runit/output/variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/variableMetadata.tsv Sun Mar 26 17:37:12 2017 -0400 |
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| diff -r 000000000000 -r 39ccace77270 runit/plasfia/plasFIA.zip |
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| diff -r 000000000000 -r 39ccace77270 runit/profia_runtests.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/profia_runtests.R Sun Mar 26 17:37:12 2017 -0400 |
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| @@ -0,0 +1,107 @@ +#!/usr/bin/env Rscript + +## Package +##-------- + +library(RUnit) + +## Constants +##---------- + +testOutDirC <- "output" +argVc <- commandArgs(trailingOnly = FALSE) +scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)]) + + +## Functions +##----------- + +## Reading tables (matrix or data frame) +readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) { + + file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\".")) + + switch(typeC, + matrix = return(t(as.matrix(read.table(file = fileC, + header = TRUE, + row.names = 1, + sep = "\t", + stringsAsFactors = FALSE)))), + dataframe = return(read.table(file = fileC, + header = TRUE, + row.names = 1, + sep = "\t", + stringsAsFactors = FALSE))) + +} + +## Call wrapper +wrapperCallF <- function(paramLs) { + + ## Set program path + wrapperPathC <- file.path(dirname(scriptPathC), "..", "profia_wrapper.R") + + ## Set arguments + argLs <- NULL + for (parC in names(paramLs)) + argLs <- c(argLs, parC, paramLs[[parC]]) + + ## Call + wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ") + + print(wrapperCallC) + + if(.Platform$OS.type == "windows") + wrapperCallC <- paste("Rscript", wrapperCallC) + + wrapperCodeN <- system(wrapperCallC) + + if (wrapperCodeN != 0) + stop("Error when running profia_wrapper.R.") + + ## Get output + outLs <- list() + if ("dataMatrix_out" %in% names(paramLs)) + outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix") + if ("sampleMetadata_out" %in% names(paramLs)) + outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe") + if ("variableMetadata_out" %in% names(paramLs)) + outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe") + if("information" %in% names(paramLs)) + outLs[["infVc"]] <- readLines(paramLs[["information"]]) + + return(outLs) +} + +## Setting default parameters +defaultArgF <- function(testInDirC) { + + defaultArgLs <- list() + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv"))) + defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv") + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv"))) + defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv") + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv"))) + defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv") + + defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv") + defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv") + defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv") + defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf") + defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt") + + defaultArgLs + +} + +## Main +##----- + +## Create output folder +file.exists(testOutDirC) || dir.create(testOutDirC) + +## Run tests +test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$') +isValidTestSuite(test.suite) +test.results <- runTestSuite(test.suite) +print(test.results) |
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| diff -r 000000000000 -r 39ccace77270 runit/profia_tests.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/profia_tests.R Sun Mar 26 17:37:12 2017 -0400 |
| [ |
| @@ -0,0 +1,16 @@ +test_plasfia_default <- function() { + + testDirC <- "plasfia" + argLs <- list(zipfile = "./plasfia/plasFIA.zip", + library = "NULL", + ppmN = "2", + ppmGroupN = "1", + fracGroupN = "0.1", + kI = "2") + + argLs <- c(defaultArgF(testDirC), argLs) + outLs <- wrapperCallF(argLs) + + checkEqualsNumeric(outLs[["datMN"]]["C100a", "M86.0965"], 1313797.6184402, tolerance = 1e-7) + +} |
| b |
| diff -r 000000000000 -r 39ccace77270 static/images/profia_workflowPositionImage.png |
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| Binary file static/images/profia_workflowPositionImage.png has changed |
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| diff -r 000000000000 -r 39ccace77270 static/images/profia_workingExampleImage.png |
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| Binary file static/images/profia_workingExampleImage.png has changed |
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| diff -r 000000000000 -r 39ccace77270 test-data/input-plasFIA.zip |
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| Binary file test-data/input-plasFIA.zip has changed |
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| diff -r 000000000000 -r 39ccace77270 test-data/output-dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output-dataMatrix.tsv Sun Mar 26 17:37:12 2017 -0400 |
| b |
| b'@@ -0,0 +1,720 @@\n+dataMatrix\tC100a\tC100b\tC100c\n+M86.0965\t1313797.61844021\t2346283.61756864\t2199831.8940868\n+M89.5775\tNA\tNA\tNA\n+M89.5944\tNA\tNA\tNA\n+M89.6051\tNA\tNA\tNA\n+M90.9767\t5106007.35482488\t6564507.32105305\t6447733.55546476\n+M93.9829\tNA\tNA\tNA\n+M93.9873\tNA\tNA\tNA\n+M93.9950\tNA\tNA\tNA\n+M94.0000\tNA\tNA\tNA\n+M94.0078\tNA\tNA\tNA\n+M94.0124\tNA\tNA\tNA\n+M94.0234\tNA\tNA\tNA\n+M94.0262\tNA\tNA\tNA\n+M94.0321\tNA\tNA\tNA\n+M94.0362\tNA\tNA\tNA\n+M94.0401\tNA\tNA\tNA\n+M94.0425\tNA\tNA\tNA\n+M94.0437\tNA\tNA\tNA\n+M94.0552\tNA\tNA\tNA\n+M94.0991\tNA\tNA\tNA\n+M94.1052\tNA\tNA\tNA\n+M94.1167\tNA\tNA\tNA\n+M94.1242\tNA\tNA\tNA\n+M94.1339\tNA\tNA\tNA\n+M94.1356\tNA\tNA\tNA\n+M94.1397\tNA\tNA\tNA\n+M94.1445\tNA\tNA\tNA\n+M94.1538\tNA\tNA\tNA\n+M95.0604\t685629.13713184\t993375.02882652\t875626.486232038\n+M96.9218\t11555241.0234047\t11798830.9597099\t13629842.0824619\n+M97.0761\t1114447.34533038\t1167650.73440278\t987109.64945019\n+M98.9189\t3036892.14294779\t2897574.20676409\t2879965.62034251\n+M102.0550\t425296.351333251\t562287.354221277\tNA\n+M102.0914\t3405898.45991167\t3405365.30747783\tNA\n+M103.9379\tNA\tNA\tNA\n+M103.9419\tNA\tNA\tNA\n+M104.1070\tNA\tNA\tNA\n+M105.0699\t4302867.69309973\t4844241.85637734\t3733356.71721098\n+M109.0760\t7482333.50573563\t7749454.43356407\t6629390.30420811\n+M112.8957\t11121448.9424704\t11023618.7533977\t11020725.581527\n+M114.0662\t3787927.88423462\t4219228.56920995\t4175211.94282092\n+M114.8928\t2599676.24720123\t2710556.01072404\t2784568.84757635\n+M115.0542\t7559851.1229425\t7681057.45130294\t5517374.77626431\n+M116.0706\t22245233.8553328\t22803669.3222943\t23491347.9559748\n+M117.0573\t2748979.07162588\t2538668.17223273\t2174237.92100802\n+M117.0699\t5790263.22958525\t4875814.61521518\t4148891.43451485\n+M118.0651\t9770801.94760909\t9328622.47944978\t9104132.1653589\n+M118.0862\t27308207.5048995\t28200166.5313722\t29895881.538737\n+M120.0655\t2294414.34871079\t2336845.67214873\t2491247.14498326\n+M120.0808\t2872417.82916936\t2263221.21507969\t2327238.94823518\n+M120.9661\t603722.847061515\tNA\t573795.21966387\n+M121.0509\t122658259.614793\t104503127.137474\t94239375.1646403\n+M121.9045\tNA\tNA\tNA\n+M121.9232\tNA\tNA\tNA\n+M121.9247\tNA\tNA\tNA\n+M121.9269\tNA\tNA\tNA\n+M121.9333\tNA\tNA\tNA\n+M121.9391\tNA\tNA\tNA\n+M121.9520\tNA\tNA\tNA\n+M121.9738\tNA\tNA\tNA\n+M121.9760\tNA\tNA\tNA\n+M121.9938\tNA\tNA\tNA\n+M122.0100\tNA\tNA\tNA\n+M122.0542\t4513962.08223987\t3201210.5171773\t4014449.66768367\n+M122.0579\tNA\tNA\tNA\n+M122.0995\tNA\tNA\tNA\n+M122.1256\tNA\tNA\tNA\n+M122.1598\tNA\tNA\tNA\n+M126.1026\t81499099.8245328\t124635981.19873\t111163001.300936\n+M127.1059\t6012736.00869722\t5472794.82842695\t4871879.07593195\n+M128.0494\t23952127.8478598\t19058160.3422955\t17601743.7731112\n+M129.0658\t988215.070873834\t1040340.62937073\t854623.945932545\n+M130.0498\t1955847.68063145\t2232763.20934855\t2467285.5945456\n+M130.0862\t1085605.25319448\t1465336.20457251\t1829782.12060952\n+M130.1087\t319305323.249651\t290908568.308084\t265409459.287951\n+M131.0815\t596446.53961781\t691807.982855779\tNA\n+M131.1057\t3682474.54143962\t2036935.67466124\t2660637.56292433\n+M131.1120\t9785332.21473518\t8692010.96517718\t8288068.26203035\n+M132.0655\t3790320.10909363\t4035488.20961741\t4165651.60338819\n+M132.0767\t2762213.88476255\t3202180.90847702\t2909373.90206213\n+M132.1019\t58938805.9629904\t60083542.3860023\t57646862.9011984\n+M133.0971\t1526239.14803199\t1680743.18492953\t1793790.93561658\n+M133.1052\t1806771.72880841\t1958263.70045634\t2116383.2046456\n+M134.0448\t563310.367045782\t550778.627756037\tNA\n+M134.0964\t69015365.274054\t65428953.2448955\t57158814.3360672\n+M134.9884\t1350501.82892699\t1316365.41719993\tNA\n+M135.0028\t16443026.4661012\t19052105.7436914\t19213830.3866995\n+M135.0301\tNA\tNA\tNA\n+M135.0998\t3994966.42947665\t3704548.05397512\t3390018.27395486\n+M136.0757\t39193123.0686269\t35076700.2394653\t34902125.3884823\n+M137.0573\t174483.88016119\tNA\t392859.082029682\n+M137.0790\tNA\tNA\tNA\n+M138.9065\t3223615.48922233\t3546765.26098753\t3392576.37740282\n+M140.0682\t1818996.32930819\t2415629.65322842\t2917498.22244721\n+M140.9035\t2335282.31470032\t1853902.13392931\t2281789.26368724\n+M142.0651\t3906512.29507626\t3220352.83524359\t3167557.04507274\n+M142.9183\t736798.97485138\t1061687.7839917\tNA\n+M142.9480\t2307463.66917123\t225'..b'170.0318936\n+M670.2559\t1754183.64727958\t2408870.1151202\t2109061.02452055\n+M670.3738\t6636668.39355427\t6446248.74652466\t6031306.96951204\n+M671.3772\t2816636.0913067\t1798089.63237222\t2111722.2798079\n+M672.3895\t4686473.79893916\t4258496.84175044\t4166255.72826511\n+M673.1164\t1469352.7683988\t1829681.76580113\t1917560.23493875\n+M674.3685\t3809129.89511944\t3160860.00557134\t2636130.13374479\n+M676.0468\t1461863.10195596\tNA\t1377422.71456078\n+M683.0643\t1259780.56399135\t1322143.83574079\t1552769.07139395\n+M683.5431\t1732441.67345777\t2525723.18668878\t2647724.55411367\n+M685.4360\t1190057.97079061\tNA\t1419229.5914531\n+M686.4051\t32080808.6893522\t28761754.7656157\t25571217.8418349\n+M687.4083\t13246103.1481081\t13951215.1330508\t8069238.27678928\n+M688.4118\t2093118.85466739\t1814091.46550962\tNA\n+M689.0812\t1476618.84097023\t1741683.93653201\t1913192.51839009\n+M689.3530\tNA\t1238431.80913389\t1029803.46358456\n+M689.4022\t4338568.86783822\t3318258.17489864\t4213005.6754478\n+M695.0984\t1270154.44480474\t1188530.68267335\t999720.609375044\n+M703.4544\t1462246.07443563\t1816537.57340901\t2642770.85961821\n+M703.5748\t5102477.6908115\t5274750.09273895\t5185173.62570642\n+M704.3794\t4977090.82171093\t4766704.41426656\t3927234.4710448\n+M704.5783\t1626987.96032962\t1669312.71186966\t1387421.31251627\n+M705.0463\tNA\t861285.955446116\t1134434.61817021\n+M705.3826\t1789589.10109757\tNA\t1709645.14232354\n+M711.0633\tNA\t1036374.52712934\t885481.220466106\n+M711.5745\t14150222.1090017\t14102404.5952038\t15356903.5818177\n+M712.5779\t5077242.5759118\t5592716.57268192\t6845985.16047672\n+M718.6320\t4297488.07177764\t2674413.24027353\t3158446.37030282\n+M719.4284\tNA\t2127705.73067334\t1707398.52119952\n+M725.5567\t5531847.39784041\t4899114.59155239\t5881591.76830335\n+M726.5600\tNA\t1491636.74107451\t1514588.19312526\n+M739.6058\t13557326.9670239\t16321329.2589389\t16792318.9578223\n+M740.6091\t5505462.91675326\t7113386.17328623\t6438361.71719427\n+M751.4289\t3250491.94756132\t4097881.10977438\t2905108.52355567\n+M758.5692\t24171669.9177599\t26133048.4446723\t29823488.7144675\n+M759.5727\t11996299.5830951\t12396459.816729\t13725260.4161819\n+M760.5758\t2312542.05691645\t1797714.30089578\t2433944.0644655\n+M760.5849\t8704293.57954915\t9171699.09361031\t11678909.7038509\n+M760.5849_2\t8704293.57954915\t9171699.09361031\t11678909.7038509\n+M761.5882\t3494168.58240472\t3623908.83475874\t3517772.49370049\n+M780.5512\t26678287.0199592\t33917501.213975\t35599330.0192635\n+M781.5548\t13370049.3355155\t6786254.01813485\t17495405.1874264\n+M782.5673\t8275387.67127943\t13698705.3298253\t14111642.4412243\n+M783.5710\t5090990.23826268\t2775887.5304272\t6341089.95006743\n+M784.5848\t5220940.29954109\t4276780.46147111\t6260943.09565952\n+M785.5880\t1686702.15583167\t2124120.66042257\t1712214.24956577\n+M786.6004\t10857162.7919506\t8697613.9851878\t12499433.8991773\n+M787.6038\t4761674.55928992\t5879054.35089474\t7047984.21331802\n+M795.5018\t2077762.78637069\tNA\t1907175.50675846\n+M796.5253\t4271079.60468799\t3501147.38860042\t5343302.22793834\n+M796.5462\tNA\t2822281.02903116\t3224036.730931\n+M804.5512\t6633582.89013492\t8165455.97185418\t7470168.70212077\n+M805.5546\t2438210.55855297\t3663463.1635972\t3764389.21632828\n+M806.5674\t4467025.00798707\t6619742.31219476\t9583742.64770817\n+M807.5718\t1352704.42256487\t2936768.26498869\t1887270.8950478\n+M808.5826\t10891390.3423662\t15794458.1878269\t16077663.9695797\n+M809.5859\t5995718.59407245\t5735791.69055253\t7082868.29906178\n+M810.6004\t1864314.89593087\t2348128.92155743\t3928135.89388521\n+M813.6843\tNA\t773185.606064327\t1241785.9308559\n+M828.5517\t6912623.84509757\t6836612.02012318\t8339689.31073757\n+M829.5550\tNA\t2944009.16774303\t4078158.50009707\n+M832.5827\t2539235.67631783\t3231564.93949998\t3214890.3796771\n+M838.5642\t2129171.20139942\t2659697.24921949\t2476264.53702713\n+M856.5830\t5771894.46378455\t6862482.35532919\t6096656.68858823\n+M857.5866\t2219552.55506141\t2623050.99114286\t2766548.52211978\n+M918.6157\t2402815.01640448\tNA\t1809595.40049242\n+M934.6468\t5786820.15496312\t5970083.49633795\t6293149.21279938\n+M935.6502\t3318525.17212971\t4159207.90254135\t2994270.82759245\n+M952.6658\tNA\t1992166.49507342\t1589196.0912281\n' |
| b |
| diff -r 000000000000 -r 39ccace77270 test/test-profia --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test-profia Sun Mar 26 17:37:12 2017 -0400 |
| b |
| @@ -0,0 +1,16 @@ +#!/bin/bash + +# Constants {{{1 +################################################################ + +PROG_PATH=$(dirname $0) + +# MAIN {{{1 +################################################################ + +$PROG_PATH/../profia_wrapper.R zipfile $PROG_PATH/../test-data/input-plasFIA.zip ppmN 2 ppmGroupN 1 fracGroupN 0.1 kI 2 dataMatrix_out $PROG_PATH/output-dataMatrix.tsv + +if ! diff "$PROG_PATH/output-dataMatrix.tsv" "$PROG_PATH/../test-data/output-dataMatrix.tsv" ; then + echo "Incorrect output data matrix." >&2 + exit 1 +fi |
