Repository 'proteore_prot_features'
hg clone https://toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features

Changeset 12:1a4cfa7a3a27 (2019-03-11)
Previous changeset 11:8df559ad14a7 (2019-01-18) Next changeset 13:0116d444d21f (2019-03-11)
Commit message:
planemo upload commit 77279e994f5751c6cd9aa165aa0604db3d241271-dirty
modified:
add_protein_features.R
add_protein_features.xml
added:
proteore_nextprot_ref.loc.sample
tool-data/nextprot_ref_09-03-2019.tsv
tool_data_table_conf.xml.sample
removed:
tool-data/result_nextprot.txt
b
diff -r 8df559ad14a7 -r 1a4cfa7a3a27 add_protein_features.R
--- a/add_protein_features.R Fri Jan 18 04:13:47 2019 -0500
+++ b/add_protein_features.R Mon Mar 11 09:16:00 2019 -0400
b
@@ -1,6 +1,6 @@
 # Read file and return file content as data.frame
 read_file <- function(path,header){
-  file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="", check.names = F),silent=TRUE)
+  file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="", check.names = F),silent=TRUE)
   if (inherits(file,"try-error")){
     stop("File not found !")
   }else{
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diff -r 8df559ad14a7 -r 1a4cfa7a3a27 add_protein_features.xml
--- a/add_protein_features.xml Fri Jan 18 04:13:47 2019 -0500
+++ b/add_protein_features.xml Mon Mar 11 09:16:00 2019 -0400
[
@@ -1,4 +1,4 @@
-<tool id="prot_features" name="Add protein features" version="2019.01.18">
+<tool id="prot_features" name="Add protein features" version="2019.03.11">
 <description>[neXtProt]
 </description>
 <requirements>
@@ -23,7 +23,12 @@
   --localization='$Nextprot_params.localization' 
   --diseases_info='$Nextprot_params.diseases_info'  
   --output='$output'  
-  --nextprot=$__tool_directory__/tool-data/result_nextprot.txt 
+
+  #if 'nextprot_ref' in str($ref_file).split("/")
+    --nextprot="$ref_file" 
+  #else 
+    --nextprot="$__tool_directory__/$ref_file"
+  #end if 
     
 ]]></command>
 
@@ -51,9 +56,10 @@
     </when>
     <when value="file">
       <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
-      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"/> 
+      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1">
+        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+      </param>
       <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
-
     </when>
   </conditional>
 
@@ -62,7 +68,7 @@
           <option value="NextprotID" selected="false">neXtProt IDs</option>
       </param>
       <section name="Nextprot_params" title="Select features" expanded="True">
-        <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="true"> 
+        <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="false"> 
           <option value="SeqLength" selected="false">Sequence Length</option>
           <option value="MW" selected="false">Molecular Weight</option>
           <option value="IsoPoint" selected="false">Isoelectric point</option>
@@ -78,6 +84,9 @@
         <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" />
 
       </section>
+      <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
+        <options from_data_table="proteore_nextprot_ref"/>
+      </param>
 
 </inputs>
 
b
diff -r 8df559ad14a7 -r 1a4cfa7a3a27 proteore_nextprot_ref.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/proteore_nextprot_ref.loc.sample Mon Mar 11 09:16:00 2019 -0400
b
@@ -0,0 +1,2 @@
+#<id> <name> <value>
+nextprot_ref_09-03-2019 neXtProt release 09-03-2019 tool-data/nextprot_ref_09-03-2019.tsv
b
diff -r 8df559ad14a7 -r 1a4cfa7a3a27 tool-data/nextprot_ref_09-03-2019.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/nextprot_ref_09-03-2019.tsv Mon Mar 11 09:16:00 2019 -0400
b
b'@@ -0,0 +1,20400 @@\n+NextprotID\tMW\tSeqLength\tIsoPoint\tChr\tSubcellLocations\tDiseases\tTMDomains\tProteinExistence\r\n+NX_A0A024RBG1\t20434\t181\t5.99\t1\tCytoplasm\tNA\t0\tPE1\r\n+NX_A0A075B6H9\t12773\t119\t6.01\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I0\t12814\t122\t4.33\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I1\t12987\t120\t5.8\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I4\t12395\t117\t7.85\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I9\t12468\t117\t6.69\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6J1\t13277\t123\t4.75\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6J6\t12549\t115\t3.95\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6J9\t12412\t118\t4.66\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K0\t12466\t115\t4.58\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K2\t12387\t115\t5.34\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K4\t12441\t115\t4.72\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K5\t12332\t115\t6.81\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K6\t13330\t122\t5.39\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6N1\t12769\t114\t6.53\t7\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B6N2\t12175\t111\t8.52\t7\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B6N3\t12929\t115\t7.68\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6N4\t12983\t114\t5.91\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6P5\t12957\t120\t5.61\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6Q5\t12891\t118\t7.69\t14\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6R2\t12848\t117\t9.64\t14\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S2\t13143\t120\t6.53\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S4\t12835\t117\t9.22\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S5\t12712\t117\t8.5\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S6\t13215\t120\t7.79\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A075B6T6\t12838\t113\t6.17\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B6T7\t15362\t132\t9.2\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6T8\t12354\t112\t4.83\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6U4\t12598\t112\t8.39\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6V5\t12697\t113\t6.57\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6W5\t13545\t121\t8.45\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6X5\t12414\t111\t5.26\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6Y3\t2097\t20\t11\t14\tCell membrane\tNA\t0\tPE4\r\n+NX_A0A075B706\t1761\t16\t8.26\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B759\t18197\t164\t9.43\t1\tCytoplasm\tNA\t0\tPE3\r\n+NX_A0A075B767\t18208\t164\t9.19\t1\tCytoplasm\tNA\t0\tPE3\r\n+NX_A0A087WSX0\t13162\t123\t6.69\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WSY4\t13025\t118\t9.7\t3\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WSY6\t12534\t115\t5.14\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A087WSZ0\t12837\t117\t7.62\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WSZ9\t12582\t112\t8.58\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087WT01\t12043\t109\t5.7\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A087WT02\t12289\t112\t5.26\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087WT03\t12306\t109\t7.76\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A087WTH1\t11832\t108\t7.61\t16\tMembrane\tNA\t0\tPE2\r\n+NX_A0A087WTH5\t15028\t132\t8.73\t21\tMembrane\tNA\t0\tPE3\r\n+NX_A0A087WUL8\t440408\t3843\t4.53\t1\tCytoplasm\tNA\t0\tPE5\r\n+NX_A0A087WV62\t12845\t115\t6.7\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087WVF3\t62187\t549\t9.2\t17\tCell membrane\tNA\t0\tPE2\r\n+NX_A0A087WW87\t13310\t121\t4.43\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WX78\t41674\t387\t8.87\t18\tNucleus\tNA\t0\tPE5\r\n+NX_A0A087WXM9\t40829\t373\t8.65\t5\tKinetochore;Centromere\tNA\t0\tPE1\r\n+NX_A0A087WXS9\t62205\t549\t9.2\t17\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087X0M5\t13028\t115\t9.14\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087X179\t62131\t549\t9.18\t17\tCell membrane\tNA\t0\tPE2\r\n+NX_A0A087X1C5\t57489\t515\t8.7\t22\tMitochondrion;Cytoplasm;Membrane\tNA\t0\tPE5\r\n+NX_A0A087X1G2\t62171\t549\t9.23\t17\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A096LNP1\t8156\t70\t8.26\t11\tSecreted\tNA\t0\tPE2\r\n+NX_A0A096LP01\t10908\t95\t6.24\t20\tNucleoplasm;Cytosol;Membrane\tNA\t0\tPE1\r\n+NX_A0A096LP49\t114856\t1063\t9.76\t9\tNA\tNA\t0\tPE1\r\n+NX_A0A096LP55\t10752\t91\t4.39\t1\tMitochondrion inner membrane\tNA\t0\tPE3\r\n+NX_A0A096LPI5\t11989\t108\t8.8\t6\tNA\tNA\t0\tPE4\r\n+NX_A0A0A0MRZ7\t13297\t120\t4.9\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A0A0MRZ8\t12625\t115\t5.15\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A0A0MRZ9\t13446\t124\t7.76\t22\tCell m'..b'1227\t1575\t6.14\t9\tBasement membrane\tCortical malformations occipital\t0\tPE1\r\n+NX_Q9Y6N7\t180930\t1651\t5.7\t3\tAxon;Endoplasmic reticulum-Golgi intermediate compartment membrane;Cell membrane\tNA\t0\tPE1\r\n+NX_Q9Y6N8\t88451\t788\t4.83\t5\tCell membrane\tNA\t0\tPE1\r\n+NX_Q9Y6N9\t62211\t552\t5.36\t11\tCytosol;Microvillus;Cytoskeleton\tDeafness, autosomal recessive, 18A;Usher syndrome 1C\t0\tPE1\r\n+NX_Q9Y6P5\t56557\t492\t5.68\t6\tCytoplasm;Nucleolus;Nucleus\tNA\t0\tPE1\r\n+NX_Q9Y6Q1\t74576\t641\t6.62\tX\tCytosol;Perinuclear region;Spindle\tNA\t0\tPE1\r\n+NX_Q9Y6Q2\t83141\t735\t5.82\t2\tCytoplasm;Membrane\tNA\t0\tPE1\r\n+NX_Q9Y6Q3\t71209\t630\t9.26\t9\tCytoplasmic vesicle;Nucleus\tNA\t0\tPE1\r\n+NX_Q9Y6Q5\t48108\t423\t8.23\t19\tCytoplasmic vesicle;Clathrin-coated vesicle membrane;Golgi apparatus\tNA\t0\tPE1\r\n+NX_Q9Y6Q6\t66034\t616\t5.21\t18\tCytosol;Cell membrane\tPaget disease of bone 2, early-onset;Osteopetrosis, autosomal recessive 7;Familial expansile osteolysis\t0\tPE1\r\n+NX_Q9Y6Q9\t155293\t1424\t7.16\t20\tCytosol;Nucleoplasm;Nucleus;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6R0\t64891\t609\t9.1\t19\tCytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6R1\t121461\t1079\t6.35\t4\tBasolateral cell membrane\tRenal tubular acidosis, proximal, with ocular abnormalities and mental retardation\t0\tPE1\r\n+NX_Q9Y6R4\t181685\t1608\t5.94\t6\tCytosol;Perinuclear region\tNA\t0\tPE1\r\n+NX_Q9Y6R6\t96807\t833\t9.17\t19\tNucleus\tNA\t0\tPE1\r\n+NX_Q9Y6R7\t572017\t5405\t5.14\t19\tCytoskeleton;Golgi apparatus;Cell membrane;Secreted\tNA\t0\tPE1\r\n+NX_Q9Y6R9\t57368\t512\t10.27\t19\tNucleus\tNA\t0\tPE1\r\n+NX_Q9Y6S9\t60036\t549\t7.06\t14\tNucleoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6T7\t90595\t804\t8.11\t7\tCytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6U3\t80489\t715\t5.5\t7\tCytoskeleton;Podosome;Cell membrane\tNA\t0\tPE1\r\n+NX_Q9Y6U7\t41101\t377\t8.98\t22\tCytoskeleton;Nucleolus;Membrane\tNA\t0\tPE2\r\n+NX_Q9Y6V0\t560699\t5142\t6.07\t7\tNucleus speckle;Synapse;Cell membrane\tPontocerebellar hypoplasia 3\t0\tPE1\r\n+NX_Q9Y6V7\t54226\t483\t9.21\t19\tMitochondrion;Nucleolus\tNA\t0\tPE1\r\n+NX_Q9Y6W3\t92652\t813\t7.55\t3\tNucleus\tNA\t0\tPE1\r\n+NX_Q9Y6W5\t54284\t498\t5.38\t1\tCytosol;Cytoplasm;Cytoskeleton;Cell membrane;Lamellipodium\tNA\t0\tPE1\r\n+NX_Q9Y6W6\t52642\t482\t7.87\t1\tCytosol;Nucleoplasm;Nucleus;Golgi apparatus;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6W8\t22625\t199\t9.01\t2\tCell membrane;Secreted\tImmunodeficiency, common variable, 1\t0\tPE1\r\n+NX_Q9Y6X0\t175008\t1596\t9.76\t18\tCytosol;Nucleus\tSchinzel-Giedion midface retraction syndrome;Leukemia, acute myelogenous;Leukemia, juvenile myelomonocytic;Myelodysplastic syndrome;Mental retardation, autosomal dominant 29;Leukemia, chronic myeloid, atypical\t0\tPE1\r\n+NX_Q9Y6X1\t7374\t66\t11.01\t3\tEndoplasmic reticulum membrane;Endoplasmic reticulum;Cell membrane;Membrane\tNA\t0\tPE1\r\n+NX_Q9Y6X2\t68017\t628\t7.81\t1\tNucleoplasm;Nucleus speckle;Nucleus;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6X3\t69082\t613\t6.84\t19\tNucleoplasm;Nucleus;Chromosome\tNA\t0\tPE1\r\n+NX_Q9Y6X4\t74955\t670\t4.52\t5\tCytosol;Nucleus inner membrane;Nucleus envelope;Nucleus membrane\tNA\t0\tPE1\r\n+NX_Q9Y6X5\t51641\t453\t5.71\t6\tCell membrane\tNA\t0\tPE1\r\n+NX_Q9Y6X6\t206129\t1858\t6.37\t13\tCytoplasmic vesicle;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6X8\t92307\t837\t6.42\t8\tNucleoplasm;Nucleus\tNA\t0\tPE1\r\n+NX_Q9Y6X9\t117823\t1032\t8.6\t22\tCytosol;Nucleus\tCharcot-Marie-Tooth disease 2Z\t0\tPE1\r\n+NX_Q9Y6Y0\t71729\t642\t5.33\t1\tNucleoplasm;Cytoplasm;Cytoskeleton;Cytosol\tNA\t0\tPE1\r\n+NX_Q9Y6Y1\t183672\t1673\t7.29\t1\tCytosol;Cytoplasm;Nucleolus;Nucleus\tCerebellar ataxia, non-progressive, with mental retardation\t0\tPE1\r\n+NX_Q9Y6Y8\t111076\t1000\t5.35\t10\tCytoplasmic vesicle;COPII-coated vesicle membrane;Endoplasmic reticulum\tNA\t0\tPE1\r\n+NX_Q9Y6Y9\t18546\t160\t8.8\t8\tCytoplasmic vesicle;Extracellular space;Secreted\tNA\t0\tPE1\r\n+NX_Q9Y6Z2\t6189\t57\t5.98\t6\tNA\tNA\t0\tPE4\r\n+NX_Q9Y6Z4\t19411\t181\t9.48\t6\tNA\tNA\t0\tPE5\r\n+NX_Q9Y6Z5\t26128\t254\t11.81\t6\tNA\tNA\t0\tPE5\r\n+NX_Q9Y6Z7\t30705\t277\t6.96\t8\tCytoplasm;Golgi apparatus;Secreted\t3MC syndrome 3\t0\tPE1\r\n+NX_Q9YNA8\t74183\t666\t9.05\t19\tCell membrane\tNA\t0\tPE1\r\n+NX_S4R3P1\t2751\t24\t5.87\t4\tCytoplasm;Secreted\tNA\t0\tPE3\r\n+NX_S4R3Y5\t2737\t24\t7.98\t1\tCytoplasm;Secreted\tNA\t0\tPE2\r\n+NX_U3KPV4\t38754\t340\t9.39\t1\tGolgi stack membrane\tNA\t0\tPE2\r\n+NX_W5XKT8\t36333\t324\t6.15\t19\tMembrane\tNA\t0\tPE1\r\n+NX_W6CW81\t12732\t113\t5.57\t1\tNA\tNA\t0\tPE1\r\n'
b
diff -r 8df559ad14a7 -r 1a4cfa7a3a27 tool-data/result_nextprot.txt
--- a/tool-data/result_nextprot.txt Fri Jan 18 04:13:47 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,20231 +0,0 @@\n-NextprotID\tMW\tSeqLength\tIsoPoint\tChr\tSubcellLocations\tDiseases\tTMDomains\tProteinExistence\n-NX_Q7RTS7\t57865\t529\t7.59\t12\tNA\tEctodermal dysplasia 7, hair/nail type;Woolly hair autosomal dominant;Hypotrichosis 3\t0\tPE1\n-NX_Q7RTS9\t75935\t669\t5.56\t18\tGolgi apparatus;Cytoplasm;Golgi apparatus;Membrane\tSmith-McCort dysplasia 1;Dyggve-Melchior-Clausen syndrome\t0\tPE1\n-NX_Q7RTT3\t21553\t188\t9.19\tX\tNA\tNA\t0\tPE2\n-NX_Q7RTT4\t21859\t187\t9.46\tX\tNA\tNA\t0\tPE2\n-NX_Q7RTT5\t21591\t188\t9.19\tX\tNA\tNA\t0\tPE2\n-NX_Q7RTT6\t21688\t188\t9.32\tX\tNA\tNA\t0\tPE5\n-NX_Q7RTT9\t58059\t530\t7.64\t7\tCytoskeleton;Cytoskeleton;Apical cell membrane;Cell membrane\tNA\t10\tPE1\n-NX_Q7RTU0\t17516\t167\t10.24\t8\tNucleus\tNA\t0\tPE3\n-NX_Q7RTU1\t23309\t214\t11.33\t2\tNucleus\tNA\t0\tPE2\n-NX_Q7RTU3\t29358\t272\t9.54\t6\tNucleus\tNA\t0\tPE1\n-NX_Q7RTU4\t24132\t235\t11.21\t17\tNucleus;Cytoplasm\tCamptosynpolydactyly, complex;Syndactyly, mesoaxial synostotic, with phalangeal reduction;Split-hand/foot malformation with long bone deficiency 3\t0\tPE1\n-NX_Q7RTU5\t29462\t278\t8.71\t1\tNucleus\tNA\t0\tPE3\n-NX_Q7RTU7\t21596\t201\t10.17\t8\tNucleus\tNA\t0\tPE3\n-NX_Q7RTU9\t192967\t1775\t5.27\t15\tKinocilium;Stereocilium;Cell surface\tDeafness, autosomal recessive, 16;Deafness-infertility syndrome\t0\tPE2\n-NX_Q7RTV0\t12405\t110\t8.79\t22\tNucleoplasm;Nucleus;Nucleus speckle\tNA\t0\tPE1\n-NX_Q7RTV2\t25722\t222\t7.74\t6\tCytoplasm\tNA\t0\tPE1\n-NX_Q7RTV3\t38411\t350\t8.07\t9\tNucleus;Nucleoplasm\tNA\t0\tPE1\n-NX_Q7RTV5\t24857\t226\t9.07\t9\tNA\tNA\t0\tPE1\n-NX_Q7RTW8\t128533\t1153\t5.53\t16\tExtracellular matrix;Apical cell membrane\tDeafness, autosomal recessive, 22\t0\tPE1\n-NX_Q7RTX0\t93386\t852\t6.75\t1\tCell membrane\tNA\t7\tPE1\n-NX_Q7RTX1\t93074\t841\t8.32\t1\tCell membrane\tNA\t7\tPE2\n-NX_Q7RTX7\t54092\t472\t5.15\t1\tFlagellum membrane\tNA\t6\tPE1\n-NX_Q7RTX9\t56254\t510\t6.45\t2\tCytosol;Cell membrane\tNA\t12\tPE2\n-NX_Q7RTY0\t44992\t426\t6.44\t17\tGolgi apparatus;Golgi apparatus membrane;Cell membrane\tDiabetes mellitus, non-insulin-dependent\t12\tPE1\n-NX_Q7RTY1\t55794\t509\t8.25\t10\tCell membrane;Cell junction;Nucleus\tNA\t12\tPE1\n-NX_Q7RTY3\t29329\t260\t8.42\t3\tNA\tNA\t0\tPE2\n-NX_Q7RTY5\t35970\t328\t7.49\t4\tSecreted\tNA\t0\tPE2\n-NX_Q7RTY7\t125066\t1134\t8.67\t12\tSecreted\tNA\t0\tPE1\n-NX_Q7RTY8\t94415\t843\t8.84\t3\tCell membrane\tNA\t1\tPE2\n-NX_Q7RTY9\t35078\t318\t9.36\t16\tCell membrane\tNA\t0\tPE1\n-NX_Q7RTZ1\t62642\t564\t7.22\t11\tSecreted\tNA\t0\tPE1\n-NX_Q7RTZ2\t59590\t530\t7.81\t8\tEndoplasmic reticulum;Nucleus\tNA\t0\tPE3\n-NX_Q7Z2D5\t82983\t763\t9\t1\tMembrane\tNA\t6\tPE1\n-NX_Q7Z2E3\t40740\t356\t9.27\t9\tCytoplasm;Nucleolus;Nucleus;Nucleoplasm;Nucleolus\tAtaxia-oculomotor apraxia syndrome\t0\tPE1\n-NX_Q7Z2F6\t14454\t126\t4.9\t16\tNucleoplasm;Cytosol\tNA\t0\tPE2\n-NX_Q7Z2G1\t19618\t175\t10.69\tX\tNucleus membrane;Chromosome\tNA\t0\tPE1\n-NX_Q7Z2H8\t53076\t476\t6.54\t5\tEndoplasmic reticulum;Cell membrane;Lysosome membrane\tNA\t11\tPE1\n-NX_Q7Z2K6\t100231\t904\t7.2\t9\tNucleus;Nucleolus;Endoplasmic reticulum membrane\tNA\t9\tPE1\n-NX_Q7Z2K8\t102399\t1008\t8.33\t5\tCell membrane;Cytoplasmic vesicle;Cell membrane;Growth cone\tNA\t0\tPE1\n-NX_Q7Z2Q7\t70301\t622\t9.02\t5\tMembrane\tNA\t1\tPE2\n-NX_Q7Z2R9\t10995\t100\t12.15\t1\tSecreted\tNA\t0\tPE5\n-NX_Q7Z2T5\t81747\t733\t8.11\t1\tNucleolus;Nucleus\tNA\t0\tPE1\n-NX_Q7Z2V1\t23111\t217\t6.41\t16\tNA\tNA\t0\tPE1\n-NX_Q7Z2W4\t101431\t902\t8.72\t7\tCytosol;Nucleus;Golgi apparatus;Cytoplasm\tNA\t0\tPE1\n-NX_Q7Z2W7\t127685\t1104\t6.91\t2\tCell membrane;Membrane raft;Endoplasmic reticulum membrane\tNA\t6\tPE1\n-NX_Q7Z2W9\t22815\t205\t9.91\t11\tNucleoplasm;Mitochondrion;Mitochondrion\tNA\t0\tPE1\n-NX_Q7Z2X4\t28272\t250\t6.53\t2\tEndoplasmic reticulum;Cytoplasm\tNA\t0\tPE1\n-NX_Q7Z2X7\t12090\t111\t4\tX\tNA\tNA\t0\tPE1\n-NX_Q7Z2Y5\t178479\t1582\t5.93\tX\tCytoplasm;Cytosol;Nucleoplasm\tNA\t0\tPE1\n-NX_Q7Z2Y8\t279048\t2422\t6.12\t11\tCytosol;Nucleus\tNA\t0\tPE2\n-NX_Q7Z2Z1\t210857\t1910\t9\t15\tNucleus;Nucleoplasm\tNA\t0\tPE1\n-NX_Q7Z2Z2\t125430\t1120\t5.66\t15\tCytosol\tNA\t0\tPE1\n-NX_Q7Z304\t77556\t686\t5.05\t9\tEndoplasmic reticulum;Extracellular matrix\tNA\t0\tPE1\n-NX_Q7Z309\t26928\t247\t5.98\tX\tNucleus;Nucleoplasm\tNA\t0\tPE1\n-NX_Q7Z333\t302880\t2677\t6.83\t9\tCytoskeleton;Nucleus;Nucleolus;Nucleus;Nucleoplasm;Cytoplasm;Chromosome;Telomere;Axon;Growth cone\tSpinocerebellar ataxia, autosomal recessive, 1;Amyotrophic lateral sclerosis 4'..b'3\t36596\t318\t8.13\t16\tCytoskeleton;Membrane;Cytosol;Nucleoplasm;Perinuclear region;Endoplasmic reticulum\tNA\t2\tPE1\n-NX_Q7L5N1\t36163\t327\t5.47\t7\tNucleus;Nucleoplasm;Nucleus;Cytoplasm\tNA\t0\tPE1\n-NX_Q7L5N7\t60208\t544\t6.14\t16\tLipid droplet;Golgi apparatus membrane;Endoplasmic reticulum membrane;Lipid droplet;Endoplasmic reticulum\tNA\t1\tPE1\n-NX_Q7L5Y1\t49786\t443\t6.03\t18\tMitochondrion\tNA\t0\tPE1\n-NX_Q7L5Y6\t63848\t550\t7.32\t15\tNucleoplasm;Cytoskeleton;Nucleus\tNA\t0\tPE1\n-NX_Q7L5Y9\t45287\t396\t8.95\t4\tNucleoplasm;Nucleus matrix;Cell membrane;Cytoskeleton\tNA\t0\tPE1\n-NX_Q7L622\t80504\t706\t7.9\t14\tCytoplasm;Nucleolus\tNA\t0\tPE1\n-NX_Q7L775\t70370\t607\t5.77\t3\tEndoplasmic reticulum\tNA\t0\tPE1\n-NX_Q7L7L0\t14121\t130\t11.05\t1\tNucleus;Chromosome\tNA\t0\tPE1\n-NX_Q7L7V1\t84419\t743\t4.88\t10\tNucleus;Mitochondrion\tNA\t0\tPE1\n-NX_Q7L7X3\t116070\t1001\t7.3\t17\tCytoplasm\tNA\t0\tPE1\n-NX_Q7L804\t58279\t512\t9.33\t10\tCytoplasmic vesicle;Nucleoplasm;Cell membrane;Recycling endosome membrane\tNA\t0\tPE1\n-NX_Q7L8A9\t40957\t365\t9.5\t14\tSecreted\tNA\t0\tPE1\n-NX_Q7L8C5\t46885\t426\t7.6\t11\tGolgi apparatus;Cytoplasmic vesicle;Membrane\tNA\t1\tPE1\n-NX_Q7L8J4\t43499\t393\t5.57\t1\tGolgi apparatus;Cytoplasmic vesicle;Nucleoplasm\tNA\t0\tPE1\n-NX_Q7L8L6\t86574\t764\t8.41\t20\tMitochondrion nucleoid\tNA\t0\tPE1\n-NX_Q7L8S5\t33300\t288\t6.29\tX\tNA\tNA\t0\tPE1\n-NX_Q7L8W6\t30307\t267\t5.24\t15\tNucleus;Nucleolus\tNA\t0\tPE1\n-NX_Q7L945\t52853\t461\t9.18\t19\tNucleolus;Nucleus;Nucleus\tNA\t0\tPE1\n-NX_Q7L985\t68066\t606\t8.44\t9\tMembrane\tNA\t1\tPE1\n-NX_Q7L9B9\t62403\t569\t8.64\t7\tNucleus speckle;Cytoplasmic vesicle;Cell membrane\tNA\t0\tPE1\n-NX_Q7L9L4\t25091\t216\t6.24\t4\tCytoplasm;Nucleus\tNA\t0\tPE1\n-NX_Q7LBC6\t191581\t1761\t6.78\t5\tNucleus;Nucleoplasm\tNA\t0\tPE1\n-NX_Q7LBE3\t86988\t791\t8.47\t1\tMembrane;Nucleus;Cell junction\tNA\t13\tPE1\n-NX_Q7LBR1\t22109\t199\t7.81\t18\tNucleus;Late endosome membrane;Midbody;Cytosol;Endosome\tNA\t0\tPE1\n-NX_Q7LC44\t45316\t396\t5.45\t8\tCytoskeleton;Synapse;Cytoplasmic vesicle;Cytoskeleton;Endosome;Acrosome;Postsynaptic density;Dendrite;Dendritic spine\tNA\t0\tPE1\n-NX_Q7LDG7\t69248\t609\t7.89\t11\tSynaptosome;Ruffle membrane;Cell membrane;Cytosol\tBleeding disorder, platelet-type 18\t0\tPE1\n-NX_Q7LDI9\t74079\t666\t9.11\t7\tCell membrane\tNA\t0\tPE1\n-NX_Q7LFL8\t32977\t322\t9.27\t5\tCytosol;Nucleoplasm;Nucleus;Cytoplasm\tNA\t0\tPE1\n-NX_Q7LFX5\t64926\t561\t8.56\t10\tCentrosome;Cytosol;Golgi apparatus membrane\tNA\t1\tPE1\n-NX_Q7LG56\t40737\t351\t4.89\t8\tNucleus;Nucleoplasm;Cytoplasm;Cytosol\tProgressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant, 5;Mitochondrial DNA depletion syndrome 8A;Mitochondrial DNA depletion syndrome 8B\t0\tPE1\n-NX_Q7LGA3\t41881\t356\t8.83\t1\tMitochondrion;Golgi apparatus membrane\tNA\t1\tPE1\n-NX_Q7LGC8\t54706\t479\t8.84\t10\tCytosol;Golgi apparatus;Golgi apparatus membrane\tSpondyloepiphyseal dysplasia with congenital joint dislocations\t1\tPE1\n-NX_Q7M4L6\t46768\t423\t6.01\t15\tNucleus\tNA\t0\tPE1\n-NX_Q7RTM1\t67353\t612\t8.71\t4\tExtracellular space;Membrane\tNA\t10\tPE2\n-NX_Q7RTN6\t48369\t431\t6.02\t17\tCytosol;Nucleoplasm;Cytoplasm;Nucleus\tNA\t0\tPE1\n-NX_Q7RTP0\t34562\t329\t8.7\t15\tCell membrane;Early endosome\tSpastic paraplegia 6, autosomal dominant\t9\tPE1\n-NX_Q7RTP6\t224295\t2002\t5.43\t22\tCytosol;Cytoplasm;Cell membrane;Nucleoplasm;Cell cortex;Cilium basal body;Spindle;Midbody;Nucleus;Cytoskeleton\tNA\t0\tPE1\n-NX_Q7RTR0\t113312\t991\t6.08\t19\tCytoplasm;Inflammasome\tNA\t0\tPE1\n-NX_Q7RTR2\t114658\t1065\t8.64\t16\tCytosol;Microtubule organizing center;Cytoplasm\tNA\t0\tPE1\n-NX_Q7RTR8\t36195\t314\t9.64\t12\tMembrane;Focal adhesion;Nucleoplasm;Cytoskeleton\tNA\t7\tPE2\n-NX_Q7RTS1\t20818\t189\t11.26\t7\tNucleoplasm;Nucleus;Golgi apparatus\tNA\t0\tPE1\n-NX_Q7RTS3\t34970\t328\t5.1\t10\tNucleus;Nucleoplasm;Cytoplasm\tPancreatic agenesis 2;Pancreatic and cerebellar agenesis\t0\tPE1\n-NX_Q7RTS5\t66296\t596\t8.96\t17\tMembrane\tNA\t12\tPE1\n-NX_Q7RTS6\t62236\t562\t7.04\t17\tMembrane\tNA\t10\tPE1\n-NX_Q8WZ42\t3816030\t34350\t6.02\t2\tCytoplasm;Nucleus   Early-onset myopathy with fatal cardiomyopathy;Cardiomyopathy, familial hypertrophic 9;Cardiomyopathy, dilated 1G;Tardive tibial muscular dystrophy;Hereditary myopathy with early respiratory failure;Limb-girdle muscular dystrophy\t2J\t0\tPE1\n'
b
diff -r 8df559ad14a7 -r 1a4cfa7a3a27 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Mar 11 09:16:00 2019 -0400
b
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tables>
+    <table name='proteore_nextprot_ref' comment_char="#">
+      <columns>id, name, value</columns>
+      <file path="tool-data/proteore_nextprot_ref.loc"/>
+    </table>
+</tables>