| Previous changeset 0:216bd2a75b1d (2017-11-26) Next changeset 2:6c84a41c44d8 (2018-03-07) |
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Commit message:
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty |
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modified:
reactome_analysis.xml |
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added:
test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt test-data/Reactome_Analysis_Tools.html test-data/Reactome_Analysis_Tools_invalid_ID.txt |
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removed:
test-data/UnipIDs.txt test-data/reactome_invalide_ids.txt test-data/reactome_output.html |
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| diff -r 216bd2a75b1d -r 35cd50b8ccf2 reactome_analysis.xml --- a/reactome_analysis.xml Sun Nov 26 19:29:17 2017 -0500 +++ b/reactome_analysis.xml Fri Feb 16 03:43:58 2018 -0500 |
| [ |
| @@ -16,19 +16,15 @@ ]]></command> <inputs> <conditional name="opt"> - <param name="input" type="select" label="Input identifiers" multiple="False" > + <param name="input" type="select" label="Input identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7)" multiple="False" > <option value="text">Copy/paste your list of IDs </option> - <!--option value="file">Choose a single-column file </option--> - <option value="file">Choose a multiple-columns file </option> + <option value="file">Input file containing your identifiers</option> </param> <when value="text" > <param name="list" type="text" label="Enter list of identifiers" /> </when> - <!--when value="file" > - <param name="idfile" type="data" format="txt" label="Choose a single-column file" /> - </when--> <when value="file" > - <param name="file" type="data" format="txt, tabular" label="Choose a multiple-columns file" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" /> + <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" /> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' /> </when> @@ -42,21 +38,40 @@ <tests> <test> <conditional name="opt" > - <param name="input" value="mq" /> - <param name="file" value="UnipIDs.txt" /> - <param name="header" value="false" /> + <param name="input" value="file" /> + <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" /> + <param name="header" value="true" /> <param name="ncol" value="c1" /> </conditional> - <output name="output" file="reactome_output.html" ftype="html" /> - <output name="trash" file="reactome_invalide_ids.txt" ftype="tab" /> + <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" /> + <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" /> </test> </tests> <help><![CDATA[ Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file. **For the rows that have more than 1 ID, only the first one is taken into account** +**Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7)** -**This tool only accepts letters (a-z or A-Z), numbers (0-9) and 3 characters "." "-" "_" for IDs. If there is ID containing other than these characters, it will be removed from the queue and placed in "Invalid identifiers" file** +----- + +.. class:: infomark + +**Authors** + +Fabregat et al. 2017 PMID: 29145629 (https://www.ncbi.nlm.nih.gov/pubmed/29145629) + +Milacic et al. 2012 PMID:24213504 (https://www.ncbi.nlm.nih.gov/pubmed/24243840) + +.. class:: infomark + +**Galaxy integration** + +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, + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. ]]></help> <citations> </citations> |
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| diff -r 216bd2a75b1d -r 35cd50b8ccf2 test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt Fri Feb 16 03:43:58 2018 -0500 |
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| b'@@ -0,0 +1,152 @@\n+Protein accession number (UniProt)\tProtein name\tNumber of peptides (razor + unique)\tneXtProt_ID\tUniProt.ID\tGeneID\tMIM\tEnsembl\n+P15924\tDesmoplakin\t69\tNX_P15924\tDESP_HUMAN\t1832\t125647; 605676; 607450; 607655; 609638; 612908; 615821\tENSG00000096696\n+P02538\tKeratin, type II cytoskeletal 6A\t53\tNX_P02538\tK2C6A_HUMAN\t3853\t148041; 615726\tENSG00000205420\n+P02768\tSerum albumin\t44\tNX_P02768\tALBU_HUMAN\t213\t103600; 615999; 616000\tENSG00000163631\n+P08779\tKeratin, type I cytoskeletal 16\t29\tNX_P08779\tK1C16_HUMAN\t3868\t148067; 167200; 613000\tENSG00000186832\n+Q02413\tDesmoglein-1\t24\tNX_Q02413\tDSG1_HUMAN\t1828\t125670; 148700; 615508\tENSG00000134760\n+P07355\tAnnexin A2;Putative annexin A2-like protein\t22\tNX_P07355\tANXA2_HUMAN\t302\t151740\tENSG00000182718\n+P14923\tJunction plakoglobin\t22\tNX_P14923\tPLAK_HUMAN\t3728\t173325; 601214; 611528\tENSG00000173801\n+P02788\tLactotransferrin\t21\tNX_P02788\tTRFL_HUMAN\t4057\t150210\tENSG00000012223\n+Q9HC84\tMucin-5B\t21\tNX_Q9HC84\tMUC5B_HUMAN\t727897\t178500; 600770\tENSG00000117983\n+P29508\tSerpin B3\t20\tNX_P29508\tSPB3_HUMAN\t6317\t600517\tENSG00000057149\n+P63261\tActin, cytoplasmic 2\t19\tNX_P63261\tACTG_HUMAN\t71\t102560; 604717; 614583\tENSG00000184009\n+Q8N1N4\tKeratin, type II cytoskeletal 78\t18\tNX_Q8N1N4\tK2C78_HUMAN\t196374\t611159\tENSG00000170423\n+Q04695\tKeratin, type I cytoskeletal 17\t18\tNX_Q04695\tK1C17_HUMAN\t3872\t148069; 167210; 184500\tENSG00000128422\n+P01876\tIg alpha-1 chain C region\t16\tNX_P01876\tIGHA1_HUMAN\tNA\t146900\tENSG00000211895; ENSG00000282633\n+Q01469\tFatty acid-binding protein 5, epidermal\t15\tNX_Q01469\tFABP5_HUMAN\t2171\t605168\tENSG00000164687\n+P31944\tCaspase-14\t15\tNX_P31944\tCASPE_HUMAN\t23581\t605848; 617320\tENSG00000105141\n+P01833\tPolymeric immunoglobulin receptor\t15\tNX_P01833\tPIGR_HUMAN\t5284\t173880\tENSG00000162896\n+P06733\tAlpha-enolase\t15\tNX_P06733\tENOA_HUMAN\t2023\t172430\tENSG00000074800\n+P25311\tZinc-alpha-2-glycoprotein\t15\tNX_P25311\tZA2G_HUMAN\t563\t194460\tENSG00000160862\n+Q15149\tPlectin\t15\tNX_Q15149\tPLEC_HUMAN\t5339\t131950; 226670; 601282; 612138; 613723; 616487\tENSG00000178209\n+P19013\tKeratin, type II cytoskeletal 4\t13\tNX_P19013\tK2C4_HUMAN\tNA\t123940; 193900\tENSG00000170477\n+Q6KB66\tKeratin, type II cytoskeletal 80\t13\tNX_Q6KB66\tK2C80_HUMAN\t144501\t611161\tENSG00000167767\n+Q08188\tProtein-glutamine gamma-glutamyltransferase E\t12\tNX_Q08188\tTGM3_HUMAN\t7053\t600238; 617251\tENSG00000125780\n+P13646\tKeratin, type I cytoskeletal 13\t11\tNX_P13646\tK1C13_HUMAN\t3860\t148065; 615785\tENSG00000171401\n+Q86YZ3\tHornerin\t11\tNX_Q86YZ3\tHORN_HUMAN\t388697\t616293\tENSG00000197915\n+P04259\tKeratin, type II cytoskeletal 6B\t10\tNX_P04259\tK2C6B_HUMAN\t3854\t148042; 615728\tENSG00000185479\n+P02545\tPrelamin-A/C;Lamin-A/C\t10\tNX_P02545\tLMNA_HUMAN\t4000\t115200; 150330; 151660; 159001; 176670; 181350; 212112; 248370; 275210; 605588; 610140; 613205; 616516\tENSG00000160789\n+P04083\tAnnexin A1\t10\tNX_P04083\tANXA1_HUMAN\t301\t151690\tENSG00000135046\n+P11021\t78 kDa glucose-regulated protein\t10\tNX_P11021\tGRP78_HUMAN\t3309\t138120\tENSG00000044574\n+P02787\tSerotransferrin\t9\tNX_P02787\tTRFE_HUMAN\t7018\t190000; 209300\tENSG00000091513\n+P04040\tCatalase\t9\tNX_P04040\tCATA_HUMAN\t847\t115500; 614097\tENSG00000121691\n+P31151\tProtein S100-A7\t9\tNX_P31151\tS10A7_HUMAN\t6278\t600353\tENSG00000143556\n+P31947\t14-3-3 protein sigma\t9\tNX_P31947\t1433S_HUMAN\t2810\t601290\tENSG00000175793\n+Q96P63\tSerpin B12\t9\tNX_Q96P63\tSPB12_HUMAN\t89777\t615662\tENSG00000166634\n+P14618\tPyruvate kinase PKM\t9\tNX_P14618\tKPYM_HUMAN\t5315\t179050\tENSG00000067225\n+P60174\tTriosephosphate isomerase\t9\tNX_P60174\tTPIS_HUMAN\t7167\t190450; 615512\tENSG00000111669\n+Q06830\tPeroxiredoxin-1\t9\tNX_Q06830\tPRDX1_HUMAN\t5052\t176763\tENSG00000117450\n+P01040\tCystatin-A\t8\tNX_P01040\tCYTA_HUMAN\t1475\t184600; 607936\tENSG00000121552\n+P05089\tArginase-1\t8\tNX_P05089\tARGI1_HUMAN\t383\t207800; 608313\tENSG00000118520\n+P01834\tIg kappa chain C region\t8\tNX_P01834\tIGKC_HUMAN\tNA\t147200; 614102\tNA\n+P04406\tGlyceraldehyde-3-phosphate dehydrogenase\t8\tNX_P04406\tG3P_HUMAN\t2597\t138400\tENSG00000111640\n+P0DMV9\tHeat shock 70 kDa protein 1B\t8\tNX_P0DMV9\tHS71B_HUMAN\t3303; 3304\t140550; '..b'X_P36952\tSPB5_HUMAN\t5268\t154790\tENSG00000206075\n+P40926\tMalate dehydrogenase, mitochondrial\t3\tNX_P40926\tMDHM_HUMAN\t4191\t154100; 617339\tENSG00000146701\n+Q9Y6R7\tIgGFc-binding protein\t3\tNX_Q9Y6R7\tFCGBP_HUMAN\t8857\t617553\tENSG00000281123\n+O95274\tLy6/PLAUR domain-containing protein 3\t2\tNX_O95274\tLYPD3_HUMAN\t27076\t609484\tENSG00000124466\n+P00491\tPurine nucleoside phosphorylase\t2\tNX_P00491\tPNPH_HUMAN\t4860\t164050; 613179\tENSG00000198805\n+P04080\tCystatin-B\t2\tNX_P04080\tCYTB_HUMAN\t1476\t254800; 601145\tENSG00000160213\n+P09972\tFructose-bisphosphate aldolase C\t2\tNX_P09972\tALDOC_HUMAN\t230\t103870\tENSG00000109107\n+P19012\tKeratin, type I cytoskeletal 15\t2\tNX_P19012\tK1C15_HUMAN\t3866\t148030\tENSG00000171346\n+P20930\tFilaggrin\t2\tNX_P20930\tFILA_HUMAN\t2312\t135940; 146700; 605803\tENSG00000143631\n+Q96FX8\tp53 apoptosis effector related to PMP-22\t2\tNX_Q96FX8\tPERP_HUMAN\t64065\t609301\tENSG00000112378\n+Q9UIV8\tSerpin B13\t2\tNX_Q9UIV8\tSPB13_HUMAN\t5275\t604445\tENSG00000197641\n+P01625\tIg kappa chain V-IV region Len\t2\tNA\tNA\tNA\tNA\tNA\n+P01765\tIg heavy chain V-III region TIL\t2\tNA\tNA\tNA\tNA\tNA\n+P01766\tIg heavy chain V-III region BRO\t2\tNX_P01766\tHV313_HUMAN\tNA\tNA\tENSG00000211942; ENSG00000282286\n+P01860\tIg gamma-3 chain C region\t2\tNX_P01860\tIGHG3_HUMAN\tNA\t147120\tNA\n+P01871\tIg mu chain C region\t2\tNX_P01871\tIGHM_HUMAN\tNA\t147020; 601495\tENSG00000211899; ENSG00000282657\n+P05090\tApolipoprotein D\t2\tNX_P05090\tAPOD_HUMAN\t347\t107740\tENSG00000189058\n+P06870\tKallikrein-1\t2\tNX_P06870\tKLK1_HUMAN\t3816\t147910; 615953\tENSG00000167748\n+P07858\tCathepsin B\t2\tNX_P07858\tCATB_HUMAN\t1508\t116810\tENSG00000164733\n+P08865\t40S ribosomal protein SA\t2\tNX_P08865\tRSSA_HUMAN\t3921\t150370; 271400\tENSG00000168028\n+P11279\tLysosome-associated membrane glycoprotein 1\t2\tNX_P11279\tLAMP1_HUMAN\t3916\t153330\tENSG00000185896\n+P13473\tLysosome-associated membrane glycoprotein 2\t2\tNX_P13473\tLAMP2_HUMAN\t3920\t300257; 309060\tENSG00000005893\n+P19971\tThymidine phosphorylase\t2\tNX_P19971\tTYPH_HUMAN\t1890\t131222; 603041\tENSG00000025708\n+P23284\tPeptidyl-prolyl cis-trans isomerase B\t2\tNX_P23284\tPPIB_HUMAN\t5479\t123841; 259440\tENSG00000166794\n+P23396\t40S ribosomal protein S3\t2\tNX_P23396\tRS3_HUMAN\t6188\t600454\tENSG00000149273\n+P25705\tATP synthase subunit alpha, mitochondrial\t2\tNX_P25705\tATPA_HUMAN\t498\t164360; 615228; 616045\tENSG00000152234\n+P27482\tCalmodulin-like protein 3\t2\tNX_P27482\tCALL3_HUMAN\t810\t114184\tENSG00000178363\n+P31949\tProtein S100-A11\t2\tNX_P31949\tS10AB_HUMAN\t6282\t603114\tENSG00000163191\n+P40121\tMacrophage-capping protein\t2\tNX_P40121\tCAPG_HUMAN\t822\t153615\tENSG00000042493\n+P42357\tHistidine ammonia-lyase\t2\tNX_P42357\tHUTH_HUMAN\t3034\t235800; 609457\tENSG00000084110\n+P47756\tF-actin-capping protein subunit beta\t2\tNX_P47756\tCAPZB_HUMAN\t832\t601572\tENSG00000077549\n+P48637\tGlutathione synthetase\t2\tNX_P48637\tGSHB_HUMAN\t2937\t231900; 266130; 601002\tENSG00000100983\n+P49720\tProteasome subunit beta type-3\t2\tNX_P49720\tPSB3_HUMAN\t5691\t602176\tENSG00000277791; ENSG00000275903\n+P50395\tRab GDP dissociation inhibitor beta\t2\tNX_P50395\tGDIB_HUMAN\t2665\t600767\tENSG00000057608\n+P59998\tActin-related protein 2/3 complex subunit 4\t2\tNX_P59998\tARPC4_HUMAN\t10093\t604226\tENSG00000241553\n+P61160\tActin-related protein 2\t2\tNX_P61160\tARP2_HUMAN\t10097\t604221\tENSG00000138071\n+P61916\tEpididymal secretory protein E1\t2\tNX_P61916\tNPC2_HUMAN\t10577\t601015; 607625\tENSG00000119655\n+P04745\tAlpha-amylase 1\t23\tNX_P04745\tAMY1_HUMAN\t276; 277; 278\t104700; 104701; 104702\tENSG00000174876; ENSG00000187733; ENSG00000237763\n+Q9NZT1\tCalmodulin-like protein 5\t8\tNX_Q9NZT1\tCALL5_HUMAN\t51806\t605183\tENSG00000178372\n+P12273\tProlactin-inducible protein\t6\tNX_P12273\tPIP_HUMAN\t5304\t176720\tENSG00000159763\n+Q96DA0\tZymogen granule protein 16 homolog B\t5\tNX_Q96DA0\tZG16B_HUMAN\t124220\tNA\tENSG00000162078; ENSG00000283056\n+P01036\tCystatin-S\t5\tNX_P01036\tCYTS_HUMAN\t1472\t123857\tENSG00000101441\n+Q8TAX7\tMucin-7\t2\tNX_Q8TAX7\tMUC7_HUMAN\t4589\t158375; 600807\tENSG00000171195\n+P01037\tCystatin-SN\t2\tNX_P01037\tCYTN_HUMAN\t1469\t123855\tENSG00000170373\n+P09228\tCystatin-SA\t2\tNX_P09228\tCYTT_HUMAN\t1470\t123856\tENSG00000170369\n' |
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| diff -r 216bd2a75b1d -r 35cd50b8ccf2 test-data/Reactome_Analysis_Tools.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Reactome_Analysis_Tools.html Fri Feb 16 03:43:58 2018 -0500 |
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| @@ -0,0 +1,48 @@ +<html> + + <head> + + <title>Connection to the Reactome Analysis Service</title> + + <style> + body { + margin: 40px; + background-color: #ffffff; + text-align: center; + } + h1 { + color: #19334d; + } + p { + margin-top: 40px; + } + button { + background-color: #ccddff; + border: 2px solid #19334d; + border-radius: 4px; + color: black; + padding: 16px 32px; + margin: 4px 2px; + cursor: pointer; + } + </style> + + </head> + + <body> + + <h1>Connection to the Reactome Analysis Service</h1> + + <p>Please click the button to execute the analysis:</p> + + <form action="http://www.reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS=MjAxODAxMTYxMTQ5NDZfNjczMg%3D%3D" target="_blank"> + + <button>Analyse</button> + + </form> + + <br> <br> + + </body> + +</html> |
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| diff -r 216bd2a75b1d -r 35cd50b8ccf2 test-data/Reactome_Analysis_Tools_invalid_ID.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Reactome_Analysis_Tools_invalid_ID.txt Fri Feb 16 03:43:58 2018 -0500 |
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| @@ -0,0 +1,1 @@ + |
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| diff -r 216bd2a75b1d -r 35cd50b8ccf2 test-data/UnipIDs.txt --- a/test-data/UnipIDs.txt Sun Nov 26 19:29:17 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -P04637 -P08246 -P63244 -P10275 -P00533 -Q14524 -P05067 -P35555 -P35222 -O95273 -P00451 -P38398 -Q05086 -Q12802 -P68871 -P04585 -Q96EB6 -Q9NYL2 -P31749 -P01137 -Q5S007 -Q08379 -P02649 -P35498 -P12931 |
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| diff -r 216bd2a75b1d -r 35cd50b8ccf2 test-data/reactome_output.html --- a/test-data/reactome_output.html Sun Nov 26 19:29:17 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,48 +0,0 @@ -<html> - - <head> - - <title>Connection to the Reactome Analysis Service</title> - - <style> - body { - margin: 40px; - background-color: #ffffff; - text-align: center; - } - h1 { - color: #19334d; - } - p { - margin-top: 40px; - } - button { - background-color: #ccddff; - border: 2px solid #19334d; - border-radius: 4px; - color: black; - padding: 16px 32px; - margin: 4px 2px; - cursor: pointer; - } - </style> - - </head> - - <body> - - <h1>Connection to the Reactome Analysis Service</h1> - - <p>Please click the button to execute the analysis:</p> - - <form action="http://www.reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS=MjAxNzA4MzAwODM0MDRfMTMxNQ%3D%3D" target="_blank"> - - <button>Analyse</button> - - </form> - - <br> <br> - - </body> - -</html> |