| Previous changeset 1:bfc679370c64 (2018-02-16) Next changeset 3:57657705cd70 (2018-03-07) |
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Commit message:
planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty |
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modified:
README.rst prot_features.xml |
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added:
tool-data/result_nextprot.txt |
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| diff -r bfc679370c64 -r 6659a32876ea README.rst --- a/README.rst Fri Feb 16 04:06:16 2018 -0500 +++ b/README.rst Tue Feb 27 08:11:33 2018 -0500 |
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| @@ -1,9 +1,9 @@ Wrapper for Protein Features tool -========================= +================================= **Authors** -T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform @@ -11,7 +11,7 @@ Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. -========================= +--------------------------------- This tool add annotation (protein features) from neXtProt database (knowledge base on human proteins) to your protein IDs list. |
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| diff -r bfc679370c64 -r 6659a32876ea prot_features.xml --- a/prot_features.xml Fri Feb 16 04:06:16 2018 -0500 +++ b/prot_features.xml Tue Feb 27 08:11:33 2018 -0500 |
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| @@ -3,6 +3,7 @@ Annotate your protein list using features retrieved from neXtProt database. </description> <requirements> + <requirement type="package" version="3.4.1">R</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -11,13 +12,31 @@ #if $inputtype.filetype == "copy_paste": - Rscript $__tool_directory__/protein_features.R --inputtype=copypaste --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column=c1 --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header=None + Rscript $__tool_directory__/protein_features.R + --inputtype=copypaste + --input='$inputtype.genelist' + --nextprot=$__tool_directory__/tool-data/result_nextprot.txt + --column=c1 --header=None + --argsP1='$Nextprot_params.P1' + --argsP2='$Nextprot_params.P2' + --argsP3='$Nextprot_params.P3' + --type='$idtype' + --output='$output' #end if #if $inputtype.filetype == "file_all": - Rscript $__tool_directory__/protein_features.R --inputtype=tabfile --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column='$inputtype.column' --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header='$inputtype.header' + Rscript $__tool_directory__/protein_features.R + --inputtype=tabfile + --input='$inputtype.genelist' + --nextprot=$__tool_directory__/tool-data/result_nextprot.txt + --column='$inputtype.column' --header='$inputtype.header' + --argsP1='$Nextprot_params.P1' + --argsP2='$Nextprot_params.P2' + --argsP3='$Nextprot_params.P3' + --type='$idtype' + --output='$output' #end if @@ -112,7 +131,7 @@ **Authors** -T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform |
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| diff -r bfc679370c64 -r 6659a32876ea tool-data/result_nextprot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/result_nextprot.txt Tue Feb 27 08:11:33 2018 -0500 |
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| b'@@ -0,0 +1,20180 @@\n+NextprotID\tMW\tSeqLength\tIsoPoint\tChr\tSubcellLocations\tDiseases\tTMDomains\tProteinExistence\n+NX_A0A075B6H9\t12773\t119\t6.01\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6I0\t12814\t122\t4.33\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6I1\t12987\t120\t5.8\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6I4\t12395\t117\t7.85\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6I9\t12468\t117\t6.69\t22\tCell membrane;Secreted\tNA\t0\tPE3\n+NX_A0A075B6J1\t13277\t123\t4.75\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6J6\t12549\t115\t3.95\t22\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A075B6J9\t12412\t118\t4.66\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6K0\t12466\t115\t4.58\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6K2\t12387\t115\t5.34\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6K4\t12441\t115\t4.72\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6K6\t13330\t122\t5.39\t22\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A075B6P5\t12957\t120\t5.61\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A075B6Q5\t12891\t118\t7.69\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6R2\t12848\t117\t9.64\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6S2\t13143\t120\t6.53\t2\tCell membrane;Secreted\tNA\t0\tPE3\n+NX_A0A075B6S4\t12835\t117\t9.22\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A075B6S5\t12712\t117\t8.5\t2\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A075B6S6\t13215\t120\t7.79\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A075B759\t18197\t164\t9.43\t1\tCytoplasm\tNA\t0\tPE3\n+NX_A0A087WSX0\t13162\t123\t6.69\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A087WSY4\t13025\t118\t9.7\t14\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A087WSY6\t12534\t115\t5.14\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A087WSZ0\t12837\t117\t7.62\t2\tCell membrane;Secreted\tNA\t0\tPE1\n+NX_A0A087WTH1\t11832\t108\t7.61\t16\tMembrane\tNA\t2\tPE3\n+NX_A0A087WTH5\t15028\t132\t8.73\t21\tMembrane\tNA\t1\tPE3\n+NX_A0A087WUL8\t440408\t3843\t4.53\t1\tCytoplasm\tNA\t0\tPE5\n+NX_A0A087WVF3\t62187\t549\t9.2\t17\tCell membrane\tNA\t0\tPE2\n+NX_A0A087WW87\t13310\t121\t4.43\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A087WX78\t41674\t387\t8.87\t18\tNucleus\tNA\t0\tPE5\n+NX_A0A087WXM9\t40829\t373\t8.65\t5\tCentromere;Kinetochore\tNA\t0\tPE2\n+NX_A0A087WXS9\t62205\t549\t9.2\t17\tCell membrane\tNA\t0\tPE3\n+NX_A0A087X179\t62131\t549\t9.18\t17\tCell membrane\tNA\t0\tPE2\n+NX_A0A087X1C5\t57489\t515\t8.7\t22\tMembrane;Cytoplasm;Mitochondrion\tNA\t2\tPE5\n+NX_A0A087X1G2\t62171\t549\t9.23\t17\tCell membrane\tNA\t0\tPE3\n+NX_A0A096LP49\t114856\t1063\t9.76\t9\tNA\tNA\t0\tPE1\n+NX_A0A096LP55\t10752\t91\t4.39\t1\tMitochondrion inner membrane\tNA\t0\tPE3\n+NX_A0A096LPI5\t11989\t108\t8.8\t6\tNA\tNA\t0\tPE4\n+NX_A0A0A0MRZ7\t13297\t120\t4.9\t2\tCell membrane;Secreted\tNA\t0\tPE3\n+NX_A0A0A0MRZ8\t12625\t115\t5.15\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A0A0MRZ9\t13446\t124\t7.76\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0A0MS14\t13508\t117\t9.2\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0A0MS15\t13056\t119\t8.84\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0A0MT36\t12340\t114\t6.7\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A0A0MT76\t4776\t42\t9.53\t22\tSecreted;Cell membrane\tNA\t0\tPE4\n+NX_A0A0A0MT89\t1394\t13\t7.1\t2\tSecreted;Cell membrane\tNA\t0\tPE4\n+NX_A0A0B4J1U3\t12478\t117\t4.56\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1U7\t13481\t121\t9.3\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1V0\t12926\t119\t8.84\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1V1\t12840\t117\t8.49\t14\tCell membrane;Secreted\tNA\t0\tPE1\n+NX_A0A0B4J1V2\t13182\t119\t8.49\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1V6\t12858\t119\t9.3\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1X5\t12840\t117\t8.91\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1X8\t13077\t118\t5.28\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1Y8\t13024\t123\t6.7\t22\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1Y9\t13203\t119\t7.69\t14\tSecreted;Cell membrane\tNA\t0\tPE1\n+NX_A0A0B4J1Z2\t12989\t117\t9.1\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A0B4J2A2\t18156\t164\t9.32\t1\tCytoplasm\tNA\t0\tPE2\n+NX_A0A0B4J2D9\t12569\t117\t7.68\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A0B4J2F0\t6313\t54\t8.04\t15\tSecreted\tNA\t0\tPE1\n+NX_A0A0B4J2H0\t12660\t117\t8.64\t14\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A0C4DH24\t12430\t114\t6.7\t2\tSecreted;Cell membrane\tNA\t0\tPE3\n+NX_A0A0C4DH25\t12515\t116\t4.46\t2\tSecreted;Cell membrane\t'..b'on\tNA\t1\tPE1\n+NX_Q9Y6N8\t88451\t788\t4.83\t5\tCell membrane\tNA\t1\tPE1\n+NX_Q9Y6N9\t62211\t552\t5.36\t11\tCytoplasm;Cytosol;Cytoskeleton;Microvillus\tDeafness, autosomal recessive, 18A;Usher syndrome 1C\t0\tPE1\n+NX_Q9Y6P5\t56557\t492\t5.68\t6\tNucleus;Cytoplasm\tNA\t0\tPE1\n+NX_Q9Y6Q1\t74576\t641\t6.62\tX\tCytoplasm;Perinuclear region;Spindle\tNA\t0\tPE1\n+NX_Q9Y6Q2\t83141\t735\t5.82\t2\tCytoplasm;Membrane\tNA\t0\tPE1\n+NX_Q9Y6Q3\t71209\t630\t9.26\t9\tNucleus;Cytoplasmic vesicle;Nucleus\tNA\t0\tPE1\n+NX_Q9Y6Q5\t48108\t423\t8.23\t19\tCytoplasmic vesicle;Golgi apparatus;Clathrin-coated vesicle membrane\tNA\t0\tPE1\n+NX_Q9Y6Q6\t66034\t616\t5.21\t18\tCytoplasm;Cell membrane;Cell membrane;Mitochondrion\tPaget disease of bone 2, early-onset;Osteopetrosis, autosomal recessive 7;Familial expansile osteolysis\t1\tPE1\n+NX_Q9Y6Q9\t155293\t1424\t7.16\t20\tNucleoplasm;Cytoplasm;Cytoplasm;Nucleus\tNA\t0\tPE1\n+NX_Q9Y6R0\t64891\t609\t9.1\t19\tCytoplasm\tNA\t0\tPE1\n+NX_Q9Y6R1\t121461\t1079\t6.35\t4\tBasolateral cell membrane\tRenal tubular acidosis, proximal, with ocular abnormalities and mental retardation\t10\tPE1\n+NX_Q9Y6R4\t181685\t1608\t5.94\t6\tPerinuclear region\tNA\t0\tPE1\n+NX_Q9Y6R6\t96807\t833\t9.17\t19\tNucleus\tNA\t0\tPE2\n+NX_Q9Y6R7\t572017\t5405\t5.14\t19\tSecreted\tNA\t0\tPE1\n+NX_Q9Y6R9\t57368\t512\t10.27\t19\tNucleus\tNA\t0\tPE1\n+NX_Q9Y6S9\t60036\t549\t7.06\t14\tNucleoplasm\tNA\t0\tPE2\n+NX_Q9Y6T7\t90595\t804\t8.11\t7\tCytoplasm\tNA\t0\tPE1\n+NX_Q9Y6U3\t80489\t715\t5.5\t7\tCytoskeleton;Podosome\tNA\t0\tPE1\n+NX_Q9Y6U7\t41101\t377\t8.98\t22\tCytoskeleton;Nucleolus;Membrane\tNA\t2\tPE4\n+NX_Q9Y6V0\t553277\t5065\t6.09\t7\tSynapse\tPontocerebellar hypoplasia 3\t0\tPE1\n+NX_Q9Y6V7\t54226\t483\t9.21\t19\tNucleolus;Mitochondrion\tNA\t0\tPE1\n+NX_Q9Y6W3\t92652\t813\t7.55\t3\tNucleoplasm;Cytoplasm;Nucleus\tNA\t0\tPE1\n+NX_Q9Y6W5\t54284\t498\t5.38\t1\tCytoskeleton;Cytoplasm;Cell membrane;Cytoplasm;Cytoskeleton;Lamellipodium\tNA\t0\tPE1\n+NX_Q9Y6W6\t52642\t482\t7.87\t1\tGolgi apparatus;Nucleoplasm;Cytoplasm;Nucleus\tNA\t0\tPE1\n+NX_Q9Y6W8\t22625\t199\t9.01\t2\tCell membrane;Secreted\tImmunodeficiency, common variable, 1\t1\tPE1\n+NX_Q9Y6X0\t175008\t1596\t9.76\t18\tNucleus\tLeukemia, chronic myeloid, atypical;Leukemia, acute myelogenous;Mental retardation, autosomal dominant 29;Myelodysplastic syndrome;Leukemia, juvenile myelomonocytic;Schinzel-Giedion midface retraction syndrome\t0\tPE1\n+NX_Q9Y6X1\t7374\t66\t11.01\t3\tCell membrane;Membrane;Endoplasmic reticulum membrane;Endoplasmic reticulum\tNA\t1\tPE1\n+NX_Q9Y6X2\t68017\t628\t7.81\t1\tCytoplasm;Nucleus;Nucleus speckle\tNA\t0\tPE1\n+NX_Q9Y6X3\t69082\t613\t6.84\t19\tNucleoplasm;Nucleoplasm\tNA\t0\tPE1\n+NX_Q9Y6X4\t74955\t670\t4.52\t5\tNucleus membrane;Cytoplasm;Nucleus envelope;Nucleus inner membrane\tNA\t0\tPE1\n+NX_Q9Y6X5\t51641\t453\t5.71\t6\tCell membrane\tNA\t1\tPE1\n+NX_Q9Y6X6\t206129\t1858\t6.37\t13\tCytoplasm\tNA\t0\tPE1\n+NX_Q9Y6X8\t92307\t837\t6.42\t8\tCytoplasm;Cell membrane;Nucleoplasm;Nucleus\tNA\t0\tPE1\n+NX_Q9Y6X9\t117823\t1032\t8.6\t22\tCytoplasm;Nucleus;Nucleus;Cytosol\tCharcot-Marie-Tooth disease 2Z\t0\tPE1\n+NX_Q9Y6Y0\t71729\t642\t5.33\t1\tCytoplasm;Cytoplasm;Cytoskeleton;Nucleoplasm\tNA\t0\tPE1\n+NX_Q9Y6Y1\t183672\t1673\t7.29\t1\tNucleus;Cytoplasm;Nucleus;Cytoplasm\tCerebellar ataxia, non-progressive, with mental retardation\t0\tPE1\n+NX_Q9Y6Y8\t111076\t1000\t5.35\t10\tCytoplasmic vesicle;COPII-coated vesicle membrane;Endoplasmic reticulum\tNA\t0\tPE1\n+NX_Q9Y6Y9\t18546\t160\t8.8\t8\tCytoplasmic vesicle;Extracellular space;Secreted\tNA\t0\tPE1\n+NX_Q9Y6Z2\t6189\t57\t5.98\t6\tNA\tNA\t0\tPE4\n+NX_Q9Y6Z4\t19411\t181\t9.48\t6\tNA\tNA\t0\tPE5\n+NX_Q9Y6Z5\t26128\t254\t11.81\t6\tNA\tNA\t0\tPE5\n+NX_Q9Y6Z7\t30705\t277\t6.96\t8\tSecreted\tNA\t0\tPE1\n+NX_Q9YNA8\t74183\t666\t9.05\t19\tCell membrane\tNA\t0\tPE1\n+NX_S4R3P1\t2751\t24\t5.87\t4\tSecreted;Cytoplasm\tNA\t0\tPE3\n+NX_S4R3Y5\t2737\t24\t7.98\t1\tSecreted;Cytoplasm\tNA\t0\tPE3\n+NX_U3KPV4\t38754\t340\t9.39\t1\tGolgi stack membrane\tNA\t1\tPE2\n+NX_W5XKT8\t36333\t324\t6.15\t19\tMembrane\tNA\t1\tPE1\n+NX_Q9UGM1\t54807\t479\t6.04\t4\tPostsynaptic cell membrane;Cell membrane\tNA\t4\tPE1\n+NX_Q8WZ42\t3816030\t34350\t6.02\t2\tCytoplasm;Nucleus\tHereditary myopathy with early respiratory failure;Cardiomyopathy, familial hypertrophic 9;Cardiomyopathy, dilated 1G;Limb-girdle muscular dystrophy 2J;Early-onset myopathy with fatal cardiomyopathy\t0\tPE1\n' |