Galaxy |

Changeset 0:0c730c636867 (2015-08-07)

Next changeset 1:6ead5b32aa17 (2015-09-02)

Commit message:
planemo upload

added:
abims_CAMERA_combinexsAnnos.xml
planemo.sh
static/images/combinexsannos_variableMetadata.png
static/images/combinexsannos_workflow.png
test-data/xset.group.retcor.group.fillPeaks.annotate.negative.Rdata
test-data/xset.group.retcor.group.fillPeaks.annotate.positive.Rdata
test-data/xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv
tool_dependencies.xml

diff -r 000000000000 -r 0c730c636867 abims_CAMERA_combinexsAnnos.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_CAMERA_combinexsAnnos.xml Fri Aug 07 11:14:08 2015 -0400

[

b'@@ -0,0 +1,212 @@\n+<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.1">\n+\n+ <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</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="1.22.0">camera</requirement>\n+ <requirement type="package" version="2.1">camera_w4m_script</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+\n+ <command>\n+ CAMERA.r \n+ xfunction combinexsAnnos image_pos $image_pos image_neg $image_neg\n+ pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta && (\n+ mv variableMetadata.tsv $variableMetadata);\n+ cat xset.log\n+ </command>\n+\n+ <inputs>\n+ <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />\n+ <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />\n+ \n+ <param name="pos" type="select" label="Returned peaklist polarity mode">\n+ <option value="TRUE" selected="true">positive</option>\n+ <option value="FALSE" >negative</option>\n+ </param>\n+\n+ <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />\n+ <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />\n+ <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/>\n+ <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>\n+\n+ </inputs>\n+\n+ <outputs>\n+ <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" />\n+ \n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ \n+ <param name="image_pos" value="xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>\n+ <param name="image_neg" value="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>\n+ <param name="pos" value="TRUE"/>\n+ <param name="tol" value="2"/>\n+ <param name="ruleset" value="1,1"/>\n+ <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />\n+ </test>\n+ </tests>\n+ \n+ \n+ <help>\n+\n+.. class:: infomark\n+\n+**Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de\n+\n+.. class:: infomark\n+\n+**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]\n+\n+ | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.\n+\n+--------------------------------'..b's. The ruleset is\n+a two column matrix with includes rule indices from the rule table of both xsAnnotate objects.\n+A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and\n+xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!\n+\n+\n+\n+-----------------\n+Workflow position\n+-----------------\n+\n+\n+**Upstream tools**\n+\n+========================= ======================= ===================== ==========\n+Name Output file Format Parameter\n+========================= ======================= ===================== ==========\n+xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file \t\t\t\n+------------------------- ----------------------- --------------------- ----------\n+xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file\n+========================= ======================= ===================== ==========\n+ \n+**Downstream tools**\n+\n++---------------------------+-----------------------------------------+--------+\n+| Name | Output file | Format |\n++===========================+=========================================+========+\n+|Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular|\n++---------------------------+-----------------------------------------+--------+\n+|Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular|\n++---------------------------+-----------------------------------------+--------+\n+|Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|\n++---------------------------+-----------------------------------------+--------+\n+|Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|\n++---------------------------+-----------------------------------------+--------+\n+\n+\n+\n+The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools:\n+ | Batch_correction\n+ | Filters\n+ | Univariate\n+ | Multivariate PCA, PLS and OPLS\n+\n+\n+**General schema of the metabolomic workflow**\n+\n+.. image:: combinexsannos_workflow.png\n+\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+----------------------------+\n+| Parameter : label | Format |\n++===========================+============================+\n+| Positive RData ion mode | rdata.camera.positive |\n++---------------------------+----------------------------+\n+| Negative RData ion mode | rdata.camera.negative |\n++---------------------------+----------------------------+\n+\n+------------\n+Output files\n+------------\n+\n+xset.combinexsAnnos.variableMetadata.tsv\n+\n+ | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.\n+ | For each metabolite (row) :\n+ | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode \n+\n+xset.combinexsAnnos.Rdata\n+\n+ | Rdata file, that be used outside Galaxy in R.\n+ \n+\n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+Input files\n+-----------\n+\n+ | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**\n+ | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**\n+\n+Parameters\n+----------\n+\n+ | pos -> **positive**\n+ | tol -> **2 (default)**\n+ | ruleset -> **1,1 (default)**\n+\n+Output files\n+------------\n+\n+**Example of an xset.combinexsAnnos.variableMetadata.tsv output:**\n+\n+.. image:: combinexsannos_variableMetadata.png\n+\n+ </help>\n+\n+ <citations>\n+ <citation type="doi"> 10.1021/ac202450g</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ </citations>\n+\n+\n+</tool>\n+ \n+ \n'

diff -r 000000000000 -r 0c730c636867 planemo.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo.sh Fri Aug 07 11:14:08 2015 -0400

[

@@ -0,0 +1,1 @@
+planemo shed_init -f --name=camera_combinexsannos --owner=lecorguille --description="[W4M][GC-MS] CAMERA R Package - Preprocessing - combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html This function check annotations of ion species with the help of a sample from opposite ion mode. As first step it searches for pseudospectra from the positive and the negative sample within a retention time window. For every result the m/z differences between both samples are matched against specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion mode with recalculated annotations. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too" --category="Metabolomics"

diff -r 000000000000 -r 0c730c636867 static/images/combinexsannos_variableMetadata.png

Binary file static/images/combinexsannos_variableMetadata.png has changed

diff -r 000000000000 -r 0c730c636867 static/images/combinexsannos_workflow.png

Binary file static/images/combinexsannos_workflow.png has changed

diff -r 000000000000 -r 0c730c636867 test-data/xset.group.retcor.group.fillPeaks.annotate.negative.Rdata

Binary file test-data/xset.group.retcor.group.fillPeaks.annotate.negative.Rdata has changed

diff -r 000000000000 -r 0c730c636867 test-data/xset.group.retcor.group.fillPeaks.annotate.positive.Rdata

Binary file test-data/xset.group.retcor.group.fillPeaks.annotate.positive.Rdata has changed

diff -r 000000000000 -r 0c730c636867 test-data/xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv Fri Aug 07 11:14:08 2015 -0400

[

b'@@ -0,0 +1,443 @@\n+name\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tbio\tblank\tisotopes\tadduct\tpcgroup\tisotopes.1\tadduct.1\tpcgroup.1\tneg. Mode\tP.fold\tP.tstat\tP.pvalue\tN.fold\tN.tstat\tN.pvalue\n+M100T333\t99.7608703656017\t99.7579925622581\t99.7637481689453\t333.27937598949\t328.522653453703\t338.036098525276\t2\t2\t0\t\t\t2685\t\t[M+H]+ 98.7536\t2685\tFound [M+H]+/[M-H]-\tInf\t-1.55778367320295\t0.194281864373894\tInf\t-1.55778367320295\t0.194281864373894\n+M105T334\t104.969993591309\t104.969123840332\t104.974052429199\t334.478718537907\t324.592900472048\t337.651441387759\t3\t3\t0\t\t\t447\t\t[M+H]+ 103.963\t447\tFound [M+H]+/[M-H]-\tInf\t-2.22723998769578\t0.0898860418679983\tInf\t-2.22723998769578\t0.0898860418679983\n+M105T351\t105.068378448486\t105.067970275879\t105.068786621094\t351.386774186232\t347.221611236822\t355.551937135641\t2\t2\t0\t\t\t3997\t\t[M+H]+ 104.061\t3997\tFound [M+H]+/[M-H]-\tInf\t-1.59651904953616\t0.185608721674373\tInf\t-1.59651904953616\t0.185608721674373\n+M105T50\t104.953605944178\t104.953545099449\t104.953649972076\t50.3907155634095\t49.6178104857725\t50.9443283160701\t9\t5\t4\t\t\t2764\t\t[M+H]+ 103.946\t2764\tFound [M+H]+/[M-H]-\t10.5982737604496\t-4.05989724028937\t0.0149522950904051\t10.5982737604496\t-4.05989724028937\t0.0149522950904051\n+M107T612\t106.961769104004\t106.957008361816\t106.966850280762\t612.036721541263\t601.253270307699\t622.647860267903\t4\t2\t1\t\t\t788\t\t[M+H]+ 105.954\t788\tFound [M+H]+/[M-H]-\t1.61172067848418\t-0.435354993611172\t0.676729042644553\t1.61172067848418\t-0.435354993611172\t0.676729042644553\n+M108T158\t107.96764755249\t107.966781616211\t107.96851348877\t157.956646561526\t155.536586952915\t160.376706170137\t2\t2\t0\t\t\t2023\t\t[M+H]+ 106.96\t2023\tFound [M+H]+/[M-H]-\tInf\t-1.60266546596844\t0.184269691166154\tInf\t-1.60266546596844\t0.184269691166154\n+M109T449\t108.816116377336\t108.814308255161\t108.817924499512\t448.912893881038\t444.074090249992\t453.751697512084\t2\t0\t2\t\t\t3088\t\t[M+H]+ 107.809\t3088\tFound [M+H]+/[M-H]-\t6.03160239028391\t1.10590709850315\t0.342684415671412\t6.03160239028391\t1.10590709850315\t0.342684415671412\n+M111T338\t111.044788224338\t111.044772467703\t111.044904694196\t338.333820229404\t334.093721862283\t339.181512181095\t5\t4\t0\t\t\t4073\t\t[M+H]+ 110.038\t4073\tFound [M+H]+/[M-H]-\tInf\t-3.36915704173404\t0.0280656260833783\tInf\t-3.36915704173404\t0.0280656260833783\n+M111T51\t110.898692794353\t110.898632566322\t110.898796114692\t51.2816141527486\t50.8226098386928\t52.1310769607387\t7\t5\t2\t\t[M+K]+ 71.9347 [M+2K]2+ 143.871\t63\t\t[M+H]+ 109.891\t63\tFound [M+H]+/[M-H]-\t107.234435520687\t-4.24543895866595\t0.0131782897563633\t107.234435520687\t-4.24543895866595\t0.0131782897563633\n+M112T292\t112.051302298222\t112.051191770866\t112.051437223534\t292.479304705274\t281.990468509378\t306.031931766139\t5\t3\t0\t\t\t4962\t\t[M+H]+ 111.044\t4962\tFound [M+H]+/[M-H]-\t3.11039852357677\t-2.54193654908641\t0.0575392267614276\t3.11039852357677\t-2.54193654908641\t0.0575392267614276\n+M112T54\t112.034626289918\t112.034597639046\t112.034654940791\t54.2708182035323\t54.189059479882\t54.3525769271825\t2\t2\t0\t\t\t1882\t\t[M+H]+ 111.027\t1882\tFound [M+H]+/[M-H]-\tInf\t-1.43289475153763\t0.22517090560669\tInf\t-1.43289475153763\t0.22517090560669\n+M115T362\t115.384078451829\t115.37760925293\t115.386878791104\t361.822851128408\t349.607330357367\t373.480686196319\t4\t3\t0\t\t\t4461\t\t[M+H]+ 114.377\t4461\tFound [M+H]+/[M-H]-\t6.1389696929279\t-2.3140345769744\t0.0614626991247251\t6.1389696929279\t-2.3140345769744\t0.0614626991247251\n+M117T1003\t116.986084037063\t116.985864459183\t116.986171601532\t1003.08654761905\t1002.26449783404\t1003.37086206897\t6\t4\t2\t\t\t56\t\t[M+H]+ 115.979\t56\tFound [M+H]+/[M-H]-\t1.16186314694844\t-0.431871845029389\t0.68206694932652\t1.16186314694844\t-0.431871845029389\t0.68206694932652\n+M117T334\t117.055379354362\t117.055256466333\t117.055456904176\t333.599102436066\t323.266073818252\t345.570157046166\t6\t0\t4\t\t\t329\t\t[M+H]+ 116.048\t329\tFound [M+H]+/[M-H]-\t1.04067368497756\t0.112630170269711\t0.91507328485967\t1.04067368497756\t0.112630170269711\t0.91507328485967\n+M117T63\t117.019027709961\t117.018931618196\t117.020763384489\t62.5229250816841\t47.7978384913575\t66.9158144421358\t11\t5\t2\t\t\t210\t\t[M+H]+ 116.012\t210\tFound ['..b'9663797\t419.488400614393\t407.274452193971\t426.34541610187\t6\t2\t0\t\t\t1728\t\t[M+H]+ 85.0164\t1728\tFound [M+H]+/[M-H]-\t3.9910944370495\t-1.99764848698304\t0.087945013683814\t3.9910944370495\t-1.99764848698304\t0.087945013683814\n+M87T337\t87.0199502464982\t87.019907261533\t87.0267369890098\t336.857160220154\t328.932758486912\t344.28868709373\t7\t3\t1\t\t\t4643\t\t[M+H]+ 86.0127\t4643\tFound [M+H]+/[M-H]-\t1.0231555537257\t0.0216918661556346\t0.983578214014113\t1.0231555537257\t0.0216918661556346\t0.983578214014113\n+M88T3\t88.003937285107\t88.003870306136\t88.0039746411383\t2.71092167699327\t1.92957542883381\t3.49564865755637\t3\t2\t1\t\t\t6803\t\t[M+H]+ 86.9967\t6803\tFound [M+H]+/[M-H]-\t2.33576893925853\t-1.25666602118248\t0.24997178856222\t2.33576893925853\t-1.25666602118248\t0.24997178856222\n+M88T458\t88.0185585021973\t88.0152587890625\t88.021858215332\t457.959290701411\t452.676572903508\t463.242008499313\t2\t0\t2\t\t\t5602\t\t[M+H]+ 87.0113\t5602\tFound [M+H]+/[M-H]-\tInf\t1.44852163980223\t0.243310495086352\tInf\t1.44852163980223\t0.243310495086352\n+M89T64\t89.0243134715871\t89.024305313763\t89.0243231692396\t63.8922475455658\t63.3707071240408\t63.9963946755224\t5\t4\t1\t\t[M+H]+ 88.0182\t7\t\t[M+H]+ 88.0182\t7\tFound [M+H]+/[M-H]-\t16.1528119551747\t-1.03515204589124\t0.359042148560027\t16.1528119551747\t-1.03515204589124\t0.359042148560027\n+M91T1\t91.0033922955555\t91.0033753323285\t91.0067366323557\t1.41157542883381\t1.35357583604733\t2.35198434456501\t3\t2\t1\t\t\t1749\t\t[M+H]+ 89.9961\t1749\tFound [M+H]+/[M-H]-\t3.15067858492482\t-2.98969115607355\t0.0469844699556694\t3.15067858492482\t-2.98969115607355\t0.0469844699556694\n+M91T339\t91.0392595211286\t91.0369474170237\t91.0413033140847\t339.179079677904\t333.806024335278\t343.775887067181\t4\t2\t1\t\t\t4054\t\t[M+H]+ 90.032\t4054\tFound [M+H]+/[M-H]-\t1.27508799527139\t-0.767595915184883\t0.47263895614649\t1.27508799527139\t-0.767595915184883\t0.47263895614649\n+M91T39\t91.0058136949774\t91.0057984660018\t91.005828923953\t39.3535347020167\t37.2530586504323\t41.4540107536011\t2\t2\t0\t\t\t158\t\t[M+H]+ 89.9985\t158\tFound [M+H]+/[M-H]-\t1.92573609266283\t-2.67072815023994\t0.0381096040398106\t1.92573609266283\t-2.67072815023994\t0.0381096040398106\n+M91T423\t90.9909457133066\t90.9907158124115\t90.9913751844474\t422.858327731071\t422.212797352317\t423.368109719466\t4\t2\t2\t\t\t5339\t\t[M+H]+ 89.9837\t5339\tFound [M+H]+/[M-H]-\t1.15287316165338\t0.370332731499949\t0.735566188411213\t1.15287316165338\t0.370332731499949\t0.735566188411213\n+M91T489\t91.0061254704578\t91.0056699208023\t91.006897304032\t489.18888042301\t475.866300646512\t500.998044796665\t11\t4\t3\t\t\t5127\t\t[M+H]+ 89.9988\t5127\tFound [M+H]+/[M-H]-\t1.42711085805442\t-1.39306056669814\t0.234314698378762\t1.42711085805442\t-1.39306056669814\t0.234314698378762\n+M93T1139\t93.007435459113\t93.0074176861003\t93.0075309882347\t1138.62792777493\t1138.27211147432\t1140.13540632002\t4\t3\t1\t\t[M+Na]+ 70.0196\t1572\t\t[M+H]+ 92.0002\t1572\tFound [M+H]+/[M-H]-\t1.59009319750693\t-0.681982679785331\t0.523170237759166\t1.59009319750693\t-0.681982679785331\t0.523170237759166\n+M94T350\t94.3168182373047\t94.3153457641602\t94.3189315795898\t349.607330357367\t347.735718771342\t358.059383781547\t3\t2\t1\t\t\t1473\t\t[M+H]+ 93.3095\t1473\tFound [M+H]+/[M-H]-\t2.80229014861983\t-0.90073218215456\t0.401405710076714\t2.80229014861983\t-0.90073218215456\t0.401405710076714\n+M95T318\t95.049995288381\t95.0499807014968\t95.0500098752651\t317.554122209402\t317.280399895152\t317.827844523652\t2\t2\t0\t\t\t2905\t\t[M+H]+ 94.0427\t2905\tFound [M+H]+/[M-H]-\tInf\t-1.94473686063201\t0.12370242993634\tInf\t-1.94473686063201\t0.12370242993634\n+M95T51\t94.9248156739247\t94.9247322803157\t94.9248737933546\t51.2847918882257\t50.3907155634095\t51.7152796793536\t8\t5\t3\t\t[M+Na]+ 71.9347 [M+2Na]2+ 143.871\t63\t\t[M+H]+ 93.9175\t63\tFound [M+H]+/[M-H]-\t37.4722940942457\t-4.91560913738868\t0.00781676528602571\t37.4722940942457\t-4.91560913738868\t0.00781676528602571\n+M99T61\t98.9555595192691\t98.9554203289135\t98.9590278194966\t60.5444205123284\t48.0328368453438\t77.1960803122144\t15\t5\t1\t\t\t2597\t\t[M+H]+ 97.9483\t2597\tFound [M+H]+/[M-H]-\t203.432997864313\t-5.93938762972869\t0.00402557203229015\t203.432997864313\t-5.93938762972869\t0.00402557203229015\n'

diff -r 000000000000 -r 0c730c636867 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Aug 07 11:14:08 2015 -0400

@@ -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="camera" version="1.22.0">
+        <repository changeset_revision="4386042cb931" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="camera_w4m_script" version="2.1">
+        <repository changeset_revision="0129dc2e0e8f" name="package_camera_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>