Galaxy |

Changeset 11:e109cacd75b2 (2019-01-02)

Previous changeset 10:7b9a4ec7ec54 (2018-12-18) Next changeset 12:dbeabf9bf091 (2019-03-07)

Commit message:
planemo upload commit f91a292f92a3e75996e6f4502fa090961727c235-dirty

modified:
add_expression_data.xml
test-data/Get_annotation_RNAseq.txt

diff -r 7b9a4ec7ec54 -r e109cacd75b2 add_expression_data.xml
--- a/add_expression_data.xml Tue Dec 18 11:14:03 2018 -0500
+++ b/add_expression_data.xml Wed Jan 02 04:40:04 2019 -0500

[

@@ -1,4 +1,4 @@
-<tool id="rna_abbased_data" name="Add expression data" version="2018.12.18">
+<tool id="rna_abbased_data" name="Add expression data" version="2019.01.02">
<description> (RNAseq or Immuno-assays)[Human Protein Atlas]
</description>
<requirements>
@@ -56,7 +56,7 @@
           <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
           <option value="Antibody">Antibody reference</option>
           <option value="RNA tissue category">RNA tissue category</option>
-   <option value="Reliability (IH)">IH detection level</option>
+       <option value="Reliability (IH)">IH detection level</option>
           <option value="Reliability (IF)">IF detection level</option>
           <option value="Subcellular location">Subcellular location</option>
           <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option>
@@ -77,10 +77,10 @@
       <param name="filetype " value="file_all"/>
       <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/>
       <param name="column" value="c8"/>
-      <param name="header" value="TRUE"/>
+      <param name="header" value="true"/>
     </conditional>
     <section name="options">
-      <param name="hpaparams" value="Gene,Gene.description,Evidence,Antibody,RNA.tissue.category,Reliability.IH,Reliability.IF,Subcellular.location,RNA.TS.TPM,TPM.max.in.non.specific"/>
+      <param name="hpaparams" value="Gene,Gene description,Evidence,Antibody,RNA tissue category,Reliability (IH),Reliability (IF),Subcellular location,RNA TS TPM,TPM max in non-specific"/>
     </section>
     <output name="output" file="Get_annotation_RNAseq.txt"/>
   </test>

diff -r 7b9a4ec7ec54 -r e109cacd75b2 test-data/Get_annotation_RNAseq.txt
--- a/test-data/Get_annotation_RNAseq.txt Tue Dec 18 11:14:03 2018 -0500
+++ b/test-data/Get_annotation_RNAseq.txt Wed Jan 02 04:40:04 2019 -0500

b'@@ -1,152 +1,170 @@\n-Ensembl gene ids\tProtein.accession.number..UniProt.\tProtein.name\tNumber.of.peptides..razor...unique.\tneXtProt_ID\tUniProt.ID\tGeneID\tMIM\tGene\tGene.description\tEvidence\tAntibody\tRNA.tissue.category\tSubcellular.location\tRNA.TS.TPM\tTPM.max.in.non.specific\n-ENSG00000005893\tP13473\tLysosome-associated membrane glycoprotein 2\t2\tNX_P13473\tLAMP2_HUMAN\t3920\t300257; 309060\tLAMP2\tLysosomal-associated membrane protein 2\tEvidence at protein level\tCAB005272, HPA029100\tExpressed in all\tNA\tNA\tgallbladder: 223.9\n-ENSG00000006625\tO75223\tGamma-glutamylcyclotransferase\t6\tNX_O75223\tGGCT_HUMAN\t79017\t137170\tGGCT\tGamma-glutamylcyclotransferase\tEvidence at protein level\tHPA020735, HPA029914\tExpressed in all\tNA\tNA\tepididymis: 123.9\n-ENSG00000012223\tP02788\tLactotransferrin\t21\tNX_P02788\tTRFL_HUMAN\t4057\t150210\tLTF\tLactotransferrin\tEvidence at protein level\tCAB008646, CAB016201, HPA057177, HPA059976\tTissue enhanced\tNA\tbone marrow: 2808.6;cervix, uterine: 1024.2\tseminal vesicle: 526.7\n-ENSG00000014216\tP07384\tCalpain-1 catalytic subunit\t4\tNX_P07384\tCAN1_HUMAN\t823\t114220; 616907\tCAPN1\tCalpain 1, (mu/I) large subunit\tEvidence at protein level\tHPA005992\tExpressed in all\tCytosol\tNA\tesophagus: 245.3\n-ENSG00000021355\tP30740\tLeukocyte elastase inhibitor\t3\tNX_P30740\tILEU_HUMAN\t1992\t130135\tSERPINB1\tSerpin peptidase inhibitor, clade B (ovalbumin), member 1\tEvidence at protein level\tHPA018871, HPA052642\tExpressed in all\tNA\tNA\tesophagus: 466.2\n-ENSG00000025708\tP19971\tThymidine phosphorylase\t2\tNX_P19971\tTYPH_HUMAN\t1890\t131222; 603041\tTYMP\tThymidine phosphorylase\tEvidence at protein level\tHPA000530, HPA001072, CAB002518\tTissue enhanced\tNuclear bodies<br>Golgi apparatus\tappendix: 103.2\tspleen: 54.0\n-ENSG00000035403\tP18206\tVinculin\t4\tNX_P18206\tVINC_HUMAN\t7414\t193065; 611407; 613255\tVCL\tVinculin\tEvidence at protein level\tHPA002131, CAB002453, HPA063777\tExpressed in all\tFocal adhesion sites\tNA\tsmooth muscle: 339.0\n-ENSG00000038002\tP20933\tN(4)-(beta-N-acetylglucosaminyl)-L-asparaginase\t3\tNX_P20933\tASPG_HUMAN\t175\t208400; 613228\tAGA\tAspartylglucosaminidase\tEvidence at protein level\tHPA031415, HPA031417\tExpressed in all\tNA\tNA\tepididymis: 34.7\n-ENSG00000042493\tP40121\tMacrophage-capping protein\t2\tNX_P40121\tCAPG_HUMAN\t822\t153615\tCAPG\tCapping protein (actin filament), gelsolin-like\tEvidence at protein level\tHPA018843, HPA019080, HPA019092\tExpressed in all\tNucleus\tNA\tparathyroid gland: 233.4\n-ENSG00000044574\tP11021\t78 kDa glucose-regulated protein\t10\tNX_P11021\tGRP78_HUMAN\t3309\t138120\tHSPA5\tHeat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)\tEvidence at protein level\tCAB005221, HPA038845, HPA038846\tExpressed in all\tCytosol\tNA\tthyroid gland: 965.5\n-ENSG00000057149\tP29508\tSerpin B3\t20\tNX_P29508\tSPB3_HUMAN\t6317\t600517\tSERPINB3\tSerpin peptidase inhibitor, clade B (ovalbumin), member 3\tEvidence at protein level\tCAB018772, CAB036006, CAB036007, HPA048341, HPA049988, HPA055992\tGroup enriched\tPlasma membrane<br>Cytosol\tcervix, uterine: 297.6;esophagus: 851.2\turinary bladder: 90.5\n-ENSG00000057608\tP50395\tRab GDP dissociation inhibitor beta\t2\tNX_P50395\tGDIB_HUMAN\t2665\t600767\tGDI2\tGDP dissociation inhibitor 2\tEvidence at protein level\tHPA049290, HPA057668\tExpressed in all\tNA\tNA\tlymph node: 244.2\n-ENSG00000067225\tP14618\tPyruvate kinase PKM\t9\tNX_P14618\tKPYM_HUMAN\t5315\t179050\tPKM\tPyruvate kinase, muscle\tEvidence at protein level\tCAB019421, HPA029501\tExpressed in all\tCytosol\tNA\tskeletal muscle: 1492.7\n-ENSG00000074800\tP06733\tAlpha-enolase\t15\tNX_P06733\tENOA_HUMAN\t2023\t172430\tENO1\tEnolase 1, (alpha)\tEvidence at protein level\tCAB018614, HPA068284, CAB069394\tExpressed in all\tNucleoplasm<br>Plasma membrane<br>Cytosol\tNA\tappendix: 789.1\n-ENSG00000077549\tP47756\tF-actin-capping protein subunit beta\t2\tNX_P47756\tCAPZB_HUMAN\t832\t601572\tCAPZB\tCapping protein (actin filament) muscle Z-line, beta\tEvidence at protein level\tHPA031531, HPA056066\tExpressed in all\tNucleoplasm<br>Vesicles<br>Cytosol\tNA\tsmooth muscle: 484.4\n-ENSG00000080824\tP07900\tHeat shock protein HSP 90-alpha\t6\tNX_P07900\tH'..b'SG00000229314\tORM1\tOrosomucoid 1\tEvidence at protein level\tCAB006265, HPA046438, HPA047725, HPA057726\tTissue enriched\tApproved\tApproved\tGolgi apparatus<br>Vesicles\tliver: 10546.0\tbone marrow: 152.7\n+P0DMV9\tHeat shock 70 kDa protein 1B\t 8\tNX_P0DMV9\tHS71B_HUMAN\t3303; 3304\t140550; 603012\tENSG00000231555\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P0DMV9\tHeat shock 70 kDa protein 1B\t 8\tNX_P0DMV9\tHS71B_HUMAN\t3303; 3304\t140550; 603012\tENSG00000232804\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P04745\tAlpha-amylase 1\t23\tNX_P04745\tAMY1_HUMAN\t276; 277; 278\t104700; 104701; 104702\tENSG00000237763\tAMY1A\tAmylase, alpha 1A (salivary)\tEvidence at protein level\tCAB004310, HPA045394, HPA045399, HPA046980\tTissue enriched\tSupported\tNA\tNA\tsalivary gland: 8907.0\tcervix: 111.5\n+P59998\tActin-related protein 2/3 complex subunit 4\t 2\tNX_P59998\tARPC4_HUMAN\t10093\t604226\tENSG00000241553\tARPC4\tActin related protein 2/3 complex, subunit 4, 20kDa\tEvidence at protein level\tNA\tExpressed in all\tNA\tNA\tNA\tNA\tlymph node: 167.0\n+P68871\tHemoglobin subunit beta\t 4\tNX_P68871\tHBB_HUMAN\t3043\t140700; 141900; 603902; 603903; 611162; 613985\tENSG00000244734\tHBB\tHemoglobin, beta\tEvidence at protein level\tCAB009526, HPA043234\tTissue enriched\tSupported\tNA\tNA\tbone marrow: 78261.0\tplacenta: 8978.3\n+P26641\tElongation factor 1-gamma\t 3\tNX_P26641\tEF1G_HUMAN\t1937\t130593\tENSG00000254772\tEEF1G\tEukaryotic translation elongation factor 1 gamma\tEvidence at protein level\tHPA040688\tExpressed in all\tApproved\tApproved\tMitochondria\tNA\tovary: 2987.8\n+P00738\tHaptoglobin\t 3\tNX_P00738\tHPT_HUMAN\t3240\t140100; 614081\tENSG00000257017\tHP\tHaptoglobin\tEvidence at protein level\tCAB003787, HPA047750\tTissue enriched\tSupported\tApproved\tVesicles\tliver: 28321.0\tbone marrow: 156.1\n+Q9C075\tKeratin, type I cytoskeletal 23\t 4\tNX_Q9C075\tK1C23_HUMAN\t25984\t606194\tENSG00000263309\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P62258\t14-3-3 protein epsilon\t 4\tNX_P62258\t1433E_HUMAN\t7531\t605066\tENSG00000274474\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P49720\tProteasome subunit beta type-3\t 2\tNX_P49720\tPSB3_HUMAN\t5691\t602176\tENSG00000275903\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01857\tIg gamma-1 chain C region\t 7\tNX_P01857\tIGHG1_HUMAN\tNA\t147100; 254500\tENSG00000277633\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P49720\tProteasome subunit beta type-3\t 2\tNX_P49720\tPSB3_HUMAN\t5691\t602176\tENSG00000277791\tPSMB3\tProteasome subunit beta 3\tEvidence at protein level\tHPA042775, HPA048147\tExpressed in all\tSupported\tNA\tNA\tNA\tepididymis: 82.2\n+Q9Y6R7\tIgGFc-binding protein\t 3\tNX_Q9Y6R7\tFCGBP_HUMAN\t8857\t617553\tENSG00000281123\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01766\tIg heavy chain V-III region BRO\t 2\tNX_P01766\tHV313_HUMAN\tNA\tNA\tENSG00000282286\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01876\tIg alpha-1 chain C region\t16\tNX_P01876\tIGHA1_HUMAN\tNA\t146900\tENSG00000282633\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01871\tIg mu chain C region\t 2\tNX_P01871\tIGHM_HUMAN\tNA\t147020; 601495\tENSG00000282657\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+O43707\tAlpha-actinin-4;Alpha-actinin-1\t 6\tNX_O43707\tACTN4_HUMAN\t81\t603278; 604638\tENSG00000282844\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P47929\tGalectin-7\t 5\tNX_P47929\tLEG7_HUMAN\t3963; 653499\t600615; 617139\tENSG00000282902\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+Q96DA0\tZymogen granule protein 16 homolog B\t 5\tNX_Q96DA0\tZG16B_HUMAN\t124220\tNA\tENSG00000283056\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P47929\tGalectin-7\t 5\tNX_P47929\tLEG7_HUMAN\t3963; 653499\t600615; 617139\tENSG00000283082\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01834\tIg kappa chain C region\t 8\tNX_P01834\tIGKC_HUMAN\tNA\t147200; 614102\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01625\tIg kappa chain V-IV region Len\t 2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01765\tIg heavy chain V-III region TIL\t 2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P0CG05\tIg lambda-2 chain C regions\t 4\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P58107\tEpiplakin\t 5\tNX_P58107\tEPIPL_HUMAN\t83481\t607553\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01860\tIg gamma-3 chain C region\t 2\tNX_P01860\tIGHG3_HUMAN\tNA\t147120\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+P01623\tIg kappa chain V-III region\t 3\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n'