| Previous changeset 0:39ccace77270 (2017-03-26) Next changeset 2:3f8ae071bdda (2018-01-22) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51 |
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modified:
README.md 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 |
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removed:
build.xml test/test-profia |
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| diff -r 39ccace77270 -r 4753e64cf694 README.md --- a/README.md Sun Mar 26 17:37:12 2017 -0400 +++ b/README.md Wed May 03 10:49:08 2017 -0400 |
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| @@ -7,11 +7,11 @@ ### Description -**Version:** 3.0.0 -**Date:** 2017-03-21 +**Version:** 3.0.4 +**Date:** 2017-05-02 **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*. +**Citation:** Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. 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) @@ -38,8 +38,8 @@ ```r source("http://www.bioconductor.org/biocLite.R") biocLite("xcms") + biocLite("plasFIA") biocLite("proFIA") - biocLite("plasFIA") ``` ### Tests @@ -53,7 +53,19 @@ ### Working example -### News +### News + +###### CHANGES IN VERSION 3.0.4 + +MINOR MODIFICATION + + * Details added in the documentation + +###### CHANGES IN VERSION 3.0.2 + +NEW FEATURE + + * Parallel processing ###### CHANGES IN VERSION 3.0.0 |
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| diff -r 39ccace77270 -r 4753e64cf694 build.xml --- a/build.xml Sun Mar 26 17:37:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,87 +0,0 @@ -<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 39ccace77270 -r 4753e64cf694 profia_config.xml --- a/profia_config.xml Sun Mar 26 17:37:12 2017 -0400 +++ b/profia_config.xml Wed May 03 10:49:08 2017 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="profia" name="proFIA" version="3.0.0">\n+<tool id="profia" name="proFIA" version="3.0.4">\n <description>Preprocessing of FIA-HRMS data</description>\n \n <requirements>\n@@ -7,6 +7,8 @@\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-xcms</requirement>\n+ <requirement type="package">bioconductor-plasFIA</requirement>\n <requirement type="package">bioconductor-proFIA</requirement>\n </requirements>\n \n@@ -14,7 +16,7 @@\n <exit_code range="1:" level="fatal" />\n </stdio>\n \n- <command><![CDATA[\n+ <command>\n Rscript $__tool_directory__/profia_wrapper.R\n \n #if $inputs.input == "lib":\n@@ -33,7 +35,7 @@\n variableMetadata_out "$variableMetadata_out"\n figure "$figure"\n information "$information"\n- ]]></command>\n+ </command>\n \n <inputs>\n <conditional name="inputs">\n@@ -42,7 +44,7 @@\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+ <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file (see the details for file upload in the help section below)" />\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@@ -73,7 +75,15 @@\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+ <output name="dataMatrix_out" file="output-dataMatrix.tsv" />\n+ <output name="information">\n+ <assert_contents>\n+ <has_text text="722 groups have been done" />\n+\t <has_text text="3 samples x 644 variables" />\n+\t <has_text text="78 excluded variables (near zero variance)" />\n+ <has_text text="2101 peaks detected" />\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n \n@@ -89,7 +99,7 @@\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+Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.\n \n ---------------------------------------------------\n \n@@ -110,7 +120,7 @@\n ---------------------------------------------------\n \n ==========================================================\n-*proFIA*: Preprocessing workflow for FIA-HRMS data\n+*proFIA*: A preprocessing workflow for FIA-HRMS data\n ==========================================================\n \n -----------\n@@ -132,9 +142,9 @@\n **References**\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-| Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29.\n-| Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080.\n-| Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303.\n+| Draper J., Lloyd A., Goodacre R. and Beckmann M. (201'..b' all your conditions as sub-directories).\n+ | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories; see below).\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 **Steps for creating the zip file**\n@@ -167,33 +183,34 @@\n .. class:: warningmark\n \n VERY IMPORTANT: If you zip your files under Windows, you must use the **7Zip** software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).\n-Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):\n-arabidopsis/wild/01.raw\n-arabidopsis/mutant/01.raw\n \n+1a) Prepare a parent folder with the name of your data set (e.g., \'arabidopsis\') containing your files:\n+ | \'arabidopsis/w1.raw\'\n+ | \'arabidopsis/w2.raw\'\n+ | ...\n+ | \'arabidopsis/m1.raw\'\n+ | \'arabidopsis/m2.raw\'\n+ | ...\n+ |\n+ \n+1b) If you have several experimental conditions resulting in distinct profiles of your samples (e.g. \'wild-type\' and \'mutant\' genotypes), create subfolders for your files (e.g., \'wild\' and \'mutant\') into your parent folder:\n+ | \'arabidopsis/wild/w1.raw\'\n+ | \'arabidopsis/wild/w2.raw\'\n+ | ...\n+ | \'arabidopsis/mutant/m1.raw\'\n+ | \'arabidopsis/mutant/m2.raw\'\n+ | ...\n+ |\n+ \n **Step2: Creating a zip file**\n-Create your zip file (e.g.: arabidopsis.zip).\n+ | Zip your **parent** folder (here the \'arabidopsis\' folder) containing all the subfolders and files with **7Zip**.\n+ |\n \n **Step 3 : Uploading it to our Galaxy server**\n-If your zip file is less than 2Gb, you get use the Get Data tool to upload it.\n-Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).\n-For more informations, don\'t hesitate to send us an email at supportATworkflow4metabolomics.org).\n-\n-**Advices for converting your files for the XCMS input**\n-\n-.. class:: warningmark\n-\n-VERY IMPORTANT: your data must be in **centroid** mode. In addition, we recommend you to convert your raw files to mzXML.\n-\n-We recommend the following parameters:\n-\n-Use Filtering: **True**\n-Use Peak Picking: **True**\n-Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode\n-Use zlib: **64**\n-Binary Encoding: **64**\n-m/z Encoding: **64**\n-Intensity Encoding: **64**\n+ | If your zip file is less than 2Gb, you get use the **Upload File** tool and the **no_unzip.zip** type to upload it.\n+ | Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).\n+ | For more informations, don\'t hesitate to send us an email at supportATworkflow4metabolomics.org).\n+ |\n \n ----------\n Parameters\n@@ -258,6 +275,21 @@\n NEWS\n ----\n \n+CHANGES IN VERSION 3.0.4\n+========================\n+\n+MINOR MODIFICATION\n+\n+Details added in the documentation\n+\n+CHANGES IN VERSION 3.0.2\n+========================\n+\n+NEW FEATURE\n+\n+Parallel processing\n+\n+\n CHANGES IN VERSION 3.0.0\n ========================\n \n@@ -270,7 +302,7 @@\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+ Author = {Delabriere, Alexis and Hohenester, Ulli and Colsch, Benoit and Junot, Christophe and Fenaille, Francois and Thevenot, Etienne A},\n Journal = {submitted},\n Year = {submitted},\n Pages = {--},\n' |
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| diff -r 39ccace77270 -r 4753e64cf694 profia_wrapper.R --- a/profia_wrapper.R Sun Mar 26 17:37:12 2017 -0400 +++ b/profia_wrapper.R Wed May 03 10:49:08 2017 -0400 |
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| @@ -97,7 +97,7 @@ fiaset <- proFIAset(directory, ppm = as.numeric(argVc["ppmN"]), - parallel = FALSE) + parallel = TRUE) stpI <- stpI + 1 @@ -182,8 +182,8 @@ row.names = FALSE, sep = "\t") -samDF <- cbind.data.frame(sampleMetadata = rownames(samDF), - samDF) +samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"], + class = samDF[, "class"]) write.table(samDF, file = argVc["sampleMetadata_out"], quote = FALSE, |
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| diff -r 39ccace77270 -r 4753e64cf694 runit/output/dataMatrix.tsv --- a/runit/output/dataMatrix.tsv Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/dataMatrix.tsv Wed May 03 10:49:08 2017 -0400 |
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| b'@@ -1,39 +1,42 @@\n dataMatrix\tC100a\tC100b\tC100c\n M86.0965\t1313797.61844021\t2346283.61756864\t2199831.8940868\n+M89.5728\tNA\tNA\tNA\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+M93.9748\tNA\tNA\tNA\n+M93.9834\tNA\tNA\tNA\n+M93.9846\tNA\tNA\tNA\n M93.9873\tNA\tNA\tNA\n+M93.9889\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+M94.0174\tNA\tNA\tNA\n+M94.0209\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+M94.0412\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+M94.1227\tNA\tNA\tNA\n+M94.1401\tNA\tNA\tNA\n M94.1445\tNA\tNA\tNA\n M94.1538\tNA\tNA\tNA\n+M94.1559\tNA\tNA\tNA\n M95.0604\t685629.13713184\t993375.02882652\t875626.486232038\n-M96.9218\t11555241.0234047\t11798830.9597099\t13629842.0824619\n+M96.9218\t11555241.0234047\t11798830.9597099\t13712178.7307854\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+M103.9195\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@@ -51,45 +54,52 @@\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+M121.8984\tNA\tNA\tNA\n M121.9045\tNA\tNA\tNA\n-M121.9232\tNA\tNA\tNA\n+M121.9157\tNA\tNA\tNA\n+M121.9208\tNA\tNA\tNA\n M121.9247\tNA\tNA\tNA\n M121.9269\tNA\tNA\tNA\n+M121.9312\tNA\tNA\tNA\n M121.9333\tNA\tNA\tNA\n M121.9391\tNA\tNA\tNA\n-M121.9520\tNA\tNA\tNA\n+M121.9524\tNA\tNA\tNA\n+M121.9552\tNA\tNA\tNA\n+M121.9704\tNA\tNA\tNA\n M121.9738\tNA\tNA\tNA\n-M121.9760\tNA\tNA\tNA\n+M121.9836\tNA\tNA\tNA\n+M121.9888\tNA\tNA\tNA\n M121.9938\tNA\tNA\tNA\n-M122.0100\tNA\tNA\tNA\n+M121.9957\tNA\tNA\tNA\n+M122.0018\tNA\tNA\tNA\n+M122.0480\tNA\tNA\tNA\n M122.0542\t4513962.08223987\t3201210.5171773\t4014449.66768367\n M122.0579\tNA\tNA\tNA\n+M122.0747\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+M126.1026\t81499099.8245328\t124635981.19873\t80083019.3531485\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+M130.1087\t319305323.249651\t291519987.402727\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+M132.1019\t58938805.9629904\t60083542.3860023\t57978919.76802\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+M134.0964\t69455994.6946368\t65595158.2631852\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+M136.0757\t39193123.0686269\t35201909.1549833\t34902125.3884823\n+M137.0573\tNA\tNA\tNA\n M137.0790\tNA\tNA\tNA\n M138.9065\t3223615.48922233\t3546765.26098753\t3392576.37740282\n M140.0682\t1818996.32930819\t2415629.65322842'..b'13445.3888372\t1501212.91393093\t1537224.91922729\n-M619.5271\t11747813.7439383\t15463697.128246\t13837978.9843392\n+M619.5272\t11747813.7439383\t15463697.128246\t14337364.5464228\n M620.5304\t3761561.01993107\t4734963.03755274\t5069530.54653342\n M623.1356\t3180595.5891105\t4042278.55956248\t4228273.45887652\n M624.1388\t724343.122602858\t695987.647308726\tNA\n-M629.1524\t2572860.64592934\t2948342.74173428\t3090087.27795212\n+M629.1524\t2572860.64592934\t3105442.1556365\t3090087.27795212\n M635.5011\t3243038.04892189\t4424993.42338596\t4436907.41009134\n M637.3638\t2153320.20402197\t1829873.68603118\tNA\n M645.1048\t849221.536255017\tNA\t1006127.8677095\n-M645.1175\t2526576.40738937\t3142328.0338279\t2962154.66068822\n-M647.5584\t15067023.1938918\t16336177.8854976\t18728177.9938016\n+M645.1176\t2526576.40738937\t3142328.0338279\t2962154.66068822\n+M647.5585\t15067023.1938918\t18399786.5062587\t18552943.5720032\n M648.5619\t6254605.04424434\t8193008.61511028\t7024234.43709767\n-M651.1343\t1987468.79138313\t2507140.87094772\t2375049.76869229\n+M651.1344\t1987468.79138313\t2507140.87094772\t2760554.45889613\n M660.0821\t814437.300289444\t1534479.22412678\t562744.881718695\n M661.0824\t2398892.29202539\t2727254.79533067\t4415848.32046208\n M662.5694\t2779079.65330773\t2482375.43135903\t2480001.0808934\n@@ -659,9 +663,8 @@\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+M687.4084\t13246103.1481081\t13951215.1330508\t12857524.9844597\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@@ -686,27 +689,27 @@\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+M760.5849\t8704293.57954915\t10886827.6669751\t11678909.7038509\n+M760.5849_2\t8704293.57954915\t10886827.6669751\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+M781.5550\t13370049.3355155\t16457198.8296785\t17495405.1874264\n M782.5673\t8275387.67127943\t13698705.3298253\t14111642.4412243\n-M783.5710\t5090990.23826268\t2775887.5304272\t6341089.95006743\n+M783.5714\t5090990.23826268\t7362752.56612007\t7714528.34789568\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+M786.6004\t10857162.7919506\t12918268.1405544\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+M806.5677\tNA\t6619742.31219476\t9583742.64770817\n+M807.5712\t1352704.42256487\t2936768.26498869\t4447312.92370322\n+M808.5826\t13656852.4024354\t15794458.1878269\t16077663.9695797\n M809.5859\t5995718.59407245\t5735791.69055253\t7082868.29906178\n-M810.6004\t1864314.89593087\t2348128.92155743\t3928135.89388521\n+M810.6003\t3629141.36584462\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' |
| b |
| diff -r 39ccace77270 -r 4753e64cf694 runit/output/figure.pdf |
| b |
| Binary file runit/output/figure.pdf has changed |
| b |
| diff -r 39ccace77270 -r 4753e64cf694 runit/output/information.txt --- a/runit/output/information.txt Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/information.txt Wed May 03 10:49:08 2017 -0400 |
| b |
| @@ -1,12 +1,12 @@ -Start of the 'proFIA' Galaxy module call: Sat 25 Mar 2017 08:55:32 PM +Start of the 'proFIA' Galaxy module call: Wed 03 May 2017 01:18:28 PM files_root_directory plasFIA 1) Peak detection step ('proFIAset'): 2) Peak alignment ('group.FIA'): - 719 groups have been done . + 722 groups have been done . 3) Creating the peak table ('makeDataMatrix'): @@ -14,9 +14,9 @@ 5) Plotting ('plot'): PCA -3 samples x 648 variables +3 samples x 644 variables standard scaling of predictors -71 excluded variables (near zero variance) +78 excluded variables (near zero variance) R2X(cum) pre ort Total 1 2 0 null device @@ -25,11 +25,11 @@ 6) Printing ('show'): A "proFIAset" object containing 1 classes. Missing values have been imputed. -2161 peaks detected. -719 features have been grouped. +2101 peaks detected. +722 features have been grouped. The data matrix is avalaible. -Memory usage: 0.425 MB +Memory usage: 0.419 MB 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'): -End of 'proFIA' Galaxy module call: 2017-03-25 21:22:13 +End of 'proFIA' Galaxy module call: 2017-05-03 13:27:09 |
| b |
| diff -r 39ccace77270 -r 4753e64cf694 runit/output/sampleMetadata.tsv --- a/runit/output/sampleMetadata.tsv Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/sampleMetadata.tsv Wed May 03 10:49:08 2017 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -sampleMetadata sampleID class -1 C100a plasFIA -2 C100b plasFIA -3 C100c plasFIA +sampleMetadata samDF[, colnames(samDF) != "sampleID"] +C100a plasFIA +C100b plasFIA +C100c plasFIA |
| b |
| diff -r 39ccace77270 -r 4753e64cf694 runit/output/variableMetadata.tsv --- a/runit/output/variableMetadata.tsv Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/variableMetadata.tsv Wed May 03 10:49:08 2017 -0400 |
| b |
| b'@@ -1,720 +1,723 @@\n 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|
| b |
| diff -r 39ccace77270 -r 4753e64cf694 test/test-profia --- a/test/test-profia Sun Mar 26 17:37:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,16 +0,0 @@ -#!/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 |