# HG changeset patch
# User proteore
# Date 1518770638 18000
# Node ID 35cd50b8ccf221c4ceb4cb2699c673bb9c8cc923
# Parent  216bd2a75b1dfc8a4c4f7a8a762b132ab9418320
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty

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>
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
@@ -0,0 +1,152 @@
+Protein accession number (UniProt)	Protein name	Number of peptides (razor + unique)	neXtProt_ID	UniProt.ID	GeneID	MIM	Ensembl
+P15924	Desmoplakin	69	NX_P15924	DESP_HUMAN	1832	125647; 605676; 607450; 607655; 609638; 612908; 615821	ENSG00000096696
+P02538	Keratin, type II cytoskeletal 6A	53	NX_P02538	K2C6A_HUMAN	3853	148041; 615726	ENSG00000205420
+P02768	Serum albumin	44	NX_P02768	ALBU_HUMAN	213	103600; 615999; 616000	ENSG00000163631
+P08779	Keratin, type I cytoskeletal 16	29	NX_P08779	K1C16_HUMAN	3868	148067; 167200; 613000	ENSG00000186832
+Q02413	Desmoglein-1	24	NX_Q02413	DSG1_HUMAN	1828	125670; 148700; 615508	ENSG00000134760
+P07355	Annexin A2;Putative annexin A2-like protein	22	NX_P07355	ANXA2_HUMAN	302	151740	ENSG00000182718
+P14923	Junction plakoglobin	22	NX_P14923	PLAK_HUMAN	3728	173325; 601214; 611528	ENSG00000173801
+P02788	Lactotransferrin	21	NX_P02788	TRFL_HUMAN	4057	150210	ENSG00000012223
+Q9HC84	Mucin-5B	21	NX_Q9HC84	MUC5B_HUMAN	727897	178500; 600770	ENSG00000117983
+P29508	Serpin B3	20	NX_P29508	SPB3_HUMAN	6317	600517	ENSG00000057149
+P63261	Actin, cytoplasmic 2	19	NX_P63261	ACTG_HUMAN	71	102560; 604717; 614583	ENSG00000184009
+Q8N1N4	Keratin, type II cytoskeletal 78	18	NX_Q8N1N4	K2C78_HUMAN	196374	611159	ENSG00000170423
+Q04695	Keratin, type I cytoskeletal 17	18	NX_Q04695	K1C17_HUMAN	3872	148069; 167210; 184500	ENSG00000128422
+P01876	Ig alpha-1 chain C region	16	NX_P01876	IGHA1_HUMAN	NA	146900	ENSG00000211895; ENSG00000282633
+Q01469	Fatty acid-binding protein 5, epidermal	15	NX_Q01469	FABP5_HUMAN	2171	605168	ENSG00000164687
+P31944	Caspase-14	15	NX_P31944	CASPE_HUMAN	23581	605848; 617320	ENSG00000105141
+P01833	Polymeric immunoglobulin receptor	15	NX_P01833	PIGR_HUMAN	5284	173880	ENSG00000162896
+P06733	Alpha-enolase	15	NX_P06733	ENOA_HUMAN	2023	172430	ENSG00000074800
+P25311	Zinc-alpha-2-glycoprotein	15	NX_P25311	ZA2G_HUMAN	563	194460	ENSG00000160862
+Q15149	Plectin	15	NX_Q15149	PLEC_HUMAN	5339	131950; 226670; 601282; 612138; 613723; 616487	ENSG00000178209
+P19013	Keratin, type II cytoskeletal 4	13	NX_P19013	K2C4_HUMAN	NA	123940; 193900	ENSG00000170477
+Q6KB66	Keratin, type II cytoskeletal 80	13	NX_Q6KB66	K2C80_HUMAN	144501	611161	ENSG00000167767
+Q08188	Protein-glutamine gamma-glutamyltransferase E	12	NX_Q08188	TGM3_HUMAN	7053	600238; 617251	ENSG00000125780
+P13646	Keratin, type I cytoskeletal 13	11	NX_P13646	K1C13_HUMAN	3860	148065; 615785	ENSG00000171401
+Q86YZ3	Hornerin	11	NX_Q86YZ3	HORN_HUMAN	388697	616293	ENSG00000197915
+P04259	Keratin, type II cytoskeletal 6B	10	NX_P04259	K2C6B_HUMAN	3854	148042; 615728	ENSG00000185479
+P02545	Prelamin-A/C;Lamin-A/C	10	NX_P02545	LMNA_HUMAN	4000	115200; 150330; 151660; 159001; 176670; 181350; 212112; 248370; 275210; 605588; 610140; 613205; 616516	ENSG00000160789
+P04083	Annexin A1	10	NX_P04083	ANXA1_HUMAN	301	151690	ENSG00000135046
+P11021	78 kDa glucose-regulated protein	10	NX_P11021	GRP78_HUMAN	3309	138120	ENSG00000044574
+P02787	Serotransferrin	9	NX_P02787	TRFE_HUMAN	7018	190000; 209300	ENSG00000091513
+P04040	Catalase	9	NX_P04040	CATA_HUMAN	847	115500; 614097	ENSG00000121691
+P31151	Protein S100-A7	9	NX_P31151	S10A7_HUMAN	6278	600353	ENSG00000143556
+P31947	14-3-3 protein sigma	9	NX_P31947	1433S_HUMAN	2810	601290	ENSG00000175793
+Q96P63	Serpin B12	9	NX_Q96P63	SPB12_HUMAN	89777	615662	ENSG00000166634
+P14618	Pyruvate kinase PKM	9	NX_P14618	KPYM_HUMAN	5315	179050	ENSG00000067225
+P60174	Triosephosphate isomerase	9	NX_P60174	TPIS_HUMAN	7167	190450; 615512	ENSG00000111669
+Q06830	Peroxiredoxin-1	9	NX_Q06830	PRDX1_HUMAN	5052	176763	ENSG00000117450
+P01040	Cystatin-A	8	NX_P01040	CYTA_HUMAN	1475	184600; 607936	ENSG00000121552
+P05089	Arginase-1	8	NX_P05089	ARGI1_HUMAN	383	207800; 608313	ENSG00000118520
+P01834	Ig kappa chain C region	8	NX_P01834	IGKC_HUMAN	NA	147200; 614102	NA
+P04406	Glyceraldehyde-3-phosphate dehydrogenase	8	NX_P04406	G3P_HUMAN	2597	138400	ENSG00000111640
+P0DMV9	Heat shock 70 kDa protein 1B	8	NX_P0DMV9	HS71B_HUMAN	3303; 3304	140550; 603012	ENSG00000204388; ENSG00000224501; ENSG00000212866; ENSG00000231555; ENSG00000232804
+P13639	Elongation factor 2	8	NX_P13639	EF2_HUMAN	1938	130610; 609306	ENSG00000167658
+P35579	Myosin-9	8	NX_P35579	MYH9_HUMAN	4627	153640; 153650; 155100; 160775; 600208; 603622; 605249	ENSG00000100345
+P68371	Tubulin beta-4B chain	8	NX_P68371	TBB4B_HUMAN	10383	602660	ENSG00000188229
+Q8WVV4	Protein POF1B	8	NX_Q8WVV4	POF1B_HUMAN	79983	300603; 300604	ENSG00000124429
+O75635	Serpin B7	7	NX_O75635	SPB7_HUMAN	8710	603357; 615598	ENSG00000166396
+P01857	Ig gamma-1 chain C region	7	NX_P01857	IGHG1_HUMAN	NA	147100; 254500	ENSG00000211896; ENSG00000277633
+P61626	Lysozyme C	7	NX_P61626	LYSC_HUMAN	4069	105200; 153450	ENSG00000090382
+P68363	Tubulin alpha-1B chain	7	NX_P68363	TBA1B_HUMAN	10376	602530	ENSG00000123416
+P01009	Alpha-1-antitrypsin;Short peptide from AAT	6	NX_P01009	A1AT_HUMAN	5265	107400; 613490	ENSG00000197249
+P07900	Heat shock protein HSP 90-alpha	6	NX_P07900	HS90A_HUMAN	3320	140571	ENSG00000080824
+Q9NZH8	Interleukin-36 gamma	6	NX_Q9NZH8	IL36G_HUMAN	56300	605542	ENSG00000136688
+O43707	Alpha-actinin-4;Alpha-actinin-1	6	NX_O43707	ACTN4_HUMAN	81	603278; 604638	ENSG00000130402; ENSG00000282844
+O75223	Gamma-glutamylcyclotransferase	6	NX_O75223	GGCT_HUMAN	79017	137170	ENSG00000006625
+P00338	L-lactate dehydrogenase A chain	6	NX_P00338	LDHA_HUMAN	3939	150000; 612933	ENSG00000134333
+P07339	Cathepsin D	6	NX_P07339	CATD_HUMAN	1509	116840; 610127	ENSG00000117984
+P62987	Ubiquitin-60S ribosomal protein L40	6	NX_P62987	RL40_HUMAN	7311	191321	ENSG00000221983
+P10599	Thioredoxin	6	NX_P10599	THIO_HUMAN	7295	187700	ENSG00000136810
+Q9UGM3	Deleted in malignant brain tumors 1 protein	6	NX_Q9UGM3	DMBT1_HUMAN	1755	137800; 601969	ENSG00000187908
+Q9UI42	Carboxypeptidase A4	6	NX_Q9UI42	CBPA4_HUMAN	51200	607635	ENSG00000128510
+P47929	Galectin-7	5	NX_P47929	LEG7_HUMAN	3963; 653499	600615; 617139	ENSG00000178934; ENSG00000205076; ENSG00000282902; ENSG00000283082
+Q13867	Bleomycin hydrolase	5	NX_Q13867	BLMH_HUMAN	642	602403	ENSG00000108578
+Q6P4A8	Phospholipase B-like 1	5	NX_Q6P4A8	PLBL1_HUMAN	79887	NA	ENSG00000121316
+O75369	Filamin-B	5	NX_O75369	FLNB_HUMAN	2317	108720; 108721; 112310; 150250; 272460; 603381	ENSG00000136068
+P00441	Superoxide dismutase [Cu-Zn]	5	NX_P00441	SODC_HUMAN	6647	105400; 147450	ENSG00000142168
+P04792	Heat shock protein beta-1	5	NX_P04792	HSPB1_HUMAN	3315	602195; 606595; 608634	ENSG00000106211
+P11142	Heat shock cognate 71 kDa protein	5	NX_P11142	HSP7C_HUMAN	3312	600816	ENSG00000109971
+P58107	Epiplakin	5	NX_P58107	EPIPL_HUMAN	83481	607553	NA
+P60842	Eukaryotic initiation factor 4A-I	5	NX_P60842	IF4A1_HUMAN	1973	602641	ENSG00000161960
+P62937	Peptidyl-prolyl cis-trans isomerase A	5	NX_P62937	PPIA_HUMAN	5478	123840	ENSG00000196262
+P63104	14-3-3 protein zeta/delta	5	NX_P63104	1433Z_HUMAN	7534	601288	ENSG00000164924
+Q92820	Gamma-glutamyl hydrolase	5	NX_Q92820	GGH_HUMAN	8836	601509	ENSG00000137563
+O75342	Arachidonate 12-lipoxygenase, 12R-type	4	NX_O75342	LX12B_HUMAN	242	242100; 603741	ENSG00000179477
+P09211	Glutathione S-transferase P	4	NX_P09211	GSTP1_HUMAN	2950	134660	ENSG00000084207
+P31025	Lipocalin-1	4	NX_P31025	LCN1_HUMAN	3933	151675	ENSG00000160349
+P48594	Serpin B4	4	NX_P48594	SPB4_HUMAN	6318	600518	ENSG00000206073
+Q14574	Desmocollin-3	4	NX_Q14574	DSC3_HUMAN	1825	600271; 613102	ENSG00000134762
+Q5T750	Skin-specific protein 32	4	NX_Q5T750	XP32_HUMAN	100129271	NA	ENSG00000198854
+Q6UWP8	Suprabasin	4	NX_Q6UWP8	SBSN_HUMAN	374897	609969	ENSG00000189001
+O60911	Cathepsin L2	4	NX_O60911	CATL2_HUMAN	1515	603308	ENSG00000136943
+P00558	Phosphoglycerate kinase 1	4	NX_P00558	PGK1_HUMAN	5230	300653; 311800	ENSG00000102144
+P04075	Fructose-bisphosphate aldolase A	4	NX_P04075	ALDOA_HUMAN	226	103850; 611881	ENSG00000149925
+P07384	Calpain-1 catalytic subunit	4	NX_P07384	CAN1_HUMAN	823	114220; 616907	ENSG00000014216
+P0CG05	Ig lambda-2 chain C regions	4	NA	NA	NA	NA	NA
+P18206	Vinculin	4	NX_P18206	VINC_HUMAN	7414	193065; 611407; 613255	ENSG00000035403
+P62258	14-3-3 protein epsilon	4	NX_P62258	1433E_HUMAN	7531	605066	ENSG00000108953; ENSG00000274474
+P68871	Hemoglobin subunit beta	4	NX_P68871	HBB_HUMAN	3043	140700; 141900; 603902; 603903; 611162; 613985	ENSG00000244734
+Q9C075	Keratin, type I cytoskeletal 23	4	NX_Q9C075	K1C23_HUMAN	25984	606194	ENSG00000108244; ENSG00000263309
+A8K2U0	Alpha-2-macroglobulin-like protein 1	3	NX_A8K2U0	A2ML1_HUMAN	144568	610627	ENSG00000166535
+P00738	Haptoglobin	3	NX_P00738	HPT_HUMAN	3240	140100; 614081	ENSG00000257017
+P01011	Alpha-1-antichymotrypsin	3	NX_P01011	AACT_HUMAN	12	107280	ENSG00000196136
+P02763	Alpha-1-acid glycoprotein 1	3	NX_P02763	A1AG1_HUMAN	5004	138600	ENSG00000229314
+P18510	Interleukin-1 receptor antagonist protein	3	NX_P18510	IL1RA_HUMAN	3557	147679; 612628; 612852	ENSG00000136689
+P22528	Cornifin-B	3	NX_P22528	SPR1B_HUMAN	6699	182266	ENSG00000169469
+P30740	Leukocyte elastase inhibitor	3	NX_P30740	ILEU_HUMAN	1992	130135	ENSG00000021355
+P80188	Neutrophil gelatinase-associated lipocalin	3	NX_P80188	NGAL_HUMAN	3934	600181	ENSG00000148346
+Q15828	Cystatin-M	3	NX_Q15828	CYTM_HUMAN	1474	601891	ENSG00000175315
+Q9HCY8	Protein S100-A14	3	NX_Q9HCY8	S10AE_HUMAN	57402	607986	ENSG00000189334
+P01623	Ig kappa chain V-III region	3	NA	NA	NA	NA	NA
+P01877	Ig alpha-2 chain C region	3	NX_P01877	IGHA2_HUMAN	NA	147000	ENSG00000211890
+P06396	Gelsolin	3	NX_P06396	GELS_HUMAN	2934	105120; 137350	ENSG00000148180
+P14735	Insulin-degrading enzyme	3	NX_P14735	IDE_HUMAN	3416	146680	ENSG00000119912
+P20933	N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase	3	NX_P20933	ASPG_HUMAN	175	208400; 613228	ENSG00000038002
+P25788	Proteasome subunit alpha type-3	3	NX_P25788	PSA3_HUMAN	5684	176843; 176845	ENSG00000100567
+P26641	Elongation factor 1-gamma	3	NX_P26641	EF1G_HUMAN	1937	130593	ENSG00000254772
+P36952	Serpin B5	3	NX_P36952	SPB5_HUMAN	5268	154790	ENSG00000206075
+P40926	Malate dehydrogenase, mitochondrial	3	NX_P40926	MDHM_HUMAN	4191	154100; 617339	ENSG00000146701
+Q9Y6R7	IgGFc-binding protein	3	NX_Q9Y6R7	FCGBP_HUMAN	8857	617553	ENSG00000281123
+O95274	Ly6/PLAUR domain-containing protein 3	2	NX_O95274	LYPD3_HUMAN	27076	609484	ENSG00000124466
+P00491	Purine nucleoside phosphorylase	2	NX_P00491	PNPH_HUMAN	4860	164050; 613179	ENSG00000198805
+P04080	Cystatin-B	2	NX_P04080	CYTB_HUMAN	1476	254800; 601145	ENSG00000160213
+P09972	Fructose-bisphosphate aldolase C	2	NX_P09972	ALDOC_HUMAN	230	103870	ENSG00000109107
+P19012	Keratin, type I cytoskeletal 15	2	NX_P19012	K1C15_HUMAN	3866	148030	ENSG00000171346
+P20930	Filaggrin	2	NX_P20930	FILA_HUMAN	2312	135940; 146700; 605803	ENSG00000143631
+Q96FX8	p53 apoptosis effector related to PMP-22	2	NX_Q96FX8	PERP_HUMAN	64065	609301	ENSG00000112378
+Q9UIV8	Serpin B13	2	NX_Q9UIV8	SPB13_HUMAN	5275	604445	ENSG00000197641
+P01625	Ig kappa chain V-IV region Len	2	NA	NA	NA	NA	NA
+P01765	Ig heavy chain V-III region TIL	2	NA	NA	NA	NA	NA
+P01766	Ig heavy chain V-III region BRO	2	NX_P01766	HV313_HUMAN	NA	NA	ENSG00000211942; ENSG00000282286
+P01860	Ig gamma-3 chain C region	2	NX_P01860	IGHG3_HUMAN	NA	147120	NA
+P01871	Ig mu chain C region	2	NX_P01871	IGHM_HUMAN	NA	147020; 601495	ENSG00000211899; ENSG00000282657
+P05090	Apolipoprotein D	2	NX_P05090	APOD_HUMAN	347	107740	ENSG00000189058
+P06870	Kallikrein-1	2	NX_P06870	KLK1_HUMAN	3816	147910; 615953	ENSG00000167748
+P07858	Cathepsin B	2	NX_P07858	CATB_HUMAN	1508	116810	ENSG00000164733
+P08865	40S ribosomal protein SA	2	NX_P08865	RSSA_HUMAN	3921	150370; 271400	ENSG00000168028
+P11279	Lysosome-associated membrane glycoprotein 1	2	NX_P11279	LAMP1_HUMAN	3916	153330	ENSG00000185896
+P13473	Lysosome-associated membrane glycoprotein 2	2	NX_P13473	LAMP2_HUMAN	3920	300257; 309060	ENSG00000005893
+P19971	Thymidine phosphorylase	2	NX_P19971	TYPH_HUMAN	1890	131222; 603041	ENSG00000025708
+P23284	Peptidyl-prolyl cis-trans isomerase B	2	NX_P23284	PPIB_HUMAN	5479	123841; 259440	ENSG00000166794
+P23396	40S ribosomal protein S3	2	NX_P23396	RS3_HUMAN	6188	600454	ENSG00000149273
+P25705	ATP synthase subunit alpha, mitochondrial	2	NX_P25705	ATPA_HUMAN	498	164360; 615228; 616045	ENSG00000152234
+P27482	Calmodulin-like protein 3	2	NX_P27482	CALL3_HUMAN	810	114184	ENSG00000178363
+P31949	Protein S100-A11	2	NX_P31949	S10AB_HUMAN	6282	603114	ENSG00000163191
+P40121	Macrophage-capping protein	2	NX_P40121	CAPG_HUMAN	822	153615	ENSG00000042493
+P42357	Histidine ammonia-lyase	2	NX_P42357	HUTH_HUMAN	3034	235800; 609457	ENSG00000084110
+P47756	F-actin-capping protein subunit beta	2	NX_P47756	CAPZB_HUMAN	832	601572	ENSG00000077549
+P48637	Glutathione synthetase	2	NX_P48637	GSHB_HUMAN	2937	231900; 266130; 601002	ENSG00000100983
+P49720	Proteasome subunit beta type-3	2	NX_P49720	PSB3_HUMAN	5691	602176	ENSG00000277791; ENSG00000275903
+P50395	Rab GDP dissociation inhibitor beta	2	NX_P50395	GDIB_HUMAN	2665	600767	ENSG00000057608
+P59998	Actin-related protein 2/3 complex subunit 4	2	NX_P59998	ARPC4_HUMAN	10093	604226	ENSG00000241553
+P61160	Actin-related protein 2	2	NX_P61160	ARP2_HUMAN	10097	604221	ENSG00000138071
+P61916	Epididymal secretory protein E1	2	NX_P61916	NPC2_HUMAN	10577	601015; 607625	ENSG00000119655
+P04745	Alpha-amylase 1	23	NX_P04745	AMY1_HUMAN	276; 277; 278	104700; 104701; 104702	ENSG00000174876; ENSG00000187733; ENSG00000237763
+Q9NZT1	Calmodulin-like protein 5	8	NX_Q9NZT1	CALL5_HUMAN	51806	605183	ENSG00000178372
+P12273	Prolactin-inducible protein	6	NX_P12273	PIP_HUMAN	5304	176720	ENSG00000159763
+Q96DA0	Zymogen granule protein 16 homolog B	5	NX_Q96DA0	ZG16B_HUMAN	124220	NA	ENSG00000162078; ENSG00000283056
+P01036	Cystatin-S	5	NX_P01036	CYTS_HUMAN	1472	123857	ENSG00000101441
+Q8TAX7	Mucin-7	2	NX_Q8TAX7	MUC7_HUMAN	4589	158375; 600807	ENSG00000171195
+P01037	Cystatin-SN	2	NX_P01037	CYTN_HUMAN	1469	123855	ENSG00000170373
+P09228	Cystatin-SA	2	NX_P09228	CYTT_HUMAN	1470	123856	ENSG00000170369
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
@@ -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>
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
@@ -0,0 +1,1 @@
+
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
@@ -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
diff -r 216bd2a75b1d -r 35cd50b8ccf2 test-data/reactome_invalide_ids.txt
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
@@ -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>