Mercurial > repos > bebatut > compute_wilcoxon_test

changeset 2:309fac5c91d8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
author bebatut
date Thu, 21 Apr 2016 04:20:40 -0400
parents ff9e8750bb26
children
files compute_wilcoxon_test.R compute_wilcoxon_test.xml test-data/input_file.txt test-data/output_file.txt test-data/two_sided_two_columns_test_output.txt
diffstat 5 files changed, 85 insertions(+), 251 deletions(-) [+]
line wrap: on
line diff
--- a/compute_wilcoxon_test.R	Thu Apr 14 10:37:32 2016 -0400
+++ b/compute_wilcoxon_test.R	Thu Apr 21 04:20:40 2016 -0400
@@ -9,12 +9,16 @@
   'paired','f',2,'logical',
   'exact','g',2,'logical',
   'correct','h',2, 'logical',
-  'mu','i',2,'integer'
+  'mu','i',2,'integer',
+  'header','y',2,'logical'
 ), byrow=TRUE, ncol=4);
 
 options = getopt(option_specification);
 
-data = read.table(options$input_file, sep = '\t', h = T)
+header = TRUE
+if(!is.null(options$header)) header = options$header
+
+data = read.table(options$input_file, sep = '\t', h = header)
 
 column1_id = 1
 if(!is.null(options$column1_id)) column1_id = options$column1_id
@@ -48,4 +52,4 @@
 m[5,] = c('alternative',test$alternative)
 m[6,] = c('method',test$method)
 write.table(m, file = options$output_file, sep = "\t", quote = FALSE, 
-    row.names = FALSE, col.names = FALSE)
\ No newline at end of file
+    row.names = FALSE, col.names = FALSE)
--- a/compute_wilcoxon_test.xml	Thu Apr 14 10:37:32 2016 -0400
+++ b/compute_wilcoxon_test.xml	Thu Apr 21 04:20:40 2016 -0400
@@ -16,12 +16,13 @@
     <command><![CDATA[
         Rscript $__tool_directory__/compute_wilcoxon_test.R
             --input_file $input_file
+	    --header $header
             --output_file $output_file
             --column1_id $column1_id
 
-            #if $add_data.test == 'true':
-                --column2_id $add_data.column2_id
-                --paired $add_data.paired
+            #if $add_column.add_column_test == "true":
+                --column2_id $add_column.column2_id
+                --paired $add_column.paired
             #end if
 
             --alternative "$alternative"
@@ -35,11 +36,13 @@
     <inputs>
         <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
 
+        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
+  
         <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/>
 
-        <conditional name="add_data">
-            <param name="test" label="Add a new column?" type="select" help="(--alternative)">
-                <option value="true" selected="True">Yes</option>
+        <conditional name="add_column">
+            <param name="add_column_test" label="Add a new column?" type="select" help="(--alternative)">
+                <option value="true" selected="true">Yes</option>
                 <option value="false">No</option>
             </param>
             <when value="true">
@@ -50,7 +53,7 @@
         </conditional>
 
         <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)">
-            <option value="two.sided" selected="True">Two sided</option>
+            <option value="two.sided" selected="true">Two sided</option>
             <option value="greater">Greater</option>
             <option value="less">Less</option>
         </param>
@@ -61,30 +64,31 @@
     </inputs>
 
     <outputs>
-        <data name="output_file" format="text"
-            label="${tool.name} on ${on_string}: Wilcox test result" />
+        <data name="output_file" format="txt"  label="${tool.name} on ${on_string}: Wilcox test result" />
     </outputs>
 
     <tests>
-        <param name="input_file" value="input_file.txt" />
-        <param name="column1_id" value="2" />
-        <param name="test" value="true" />
-        <param name="column2_id" value="3" />
-        <param name="paired" value="TRUE" />
-        <param name="alternative" value="two.sided" />
-        <param name="mu" value="0" />
-        <param name="exact" value="FALSE" />
-        <param name="correct" value="TRUE"/>
-        <output name="output_file" value="output_file.txt" />
+        <test>
+            <param name="input_file" ftype="tabular" value="input_file.txt"/>
+            <param name="header" value="TRUE"/>
+            <param name="column1_id" value="3"/>
+            <param name="add_column_test" value="true"/>
+            <param name="column2_id" value="5"/>
+            <param name="paired" value="FALSE"/>
+            <param name="alternative" value="two.sided"/>
+            <param name="mu" value="0"/>
+            <param name="exact" value="FALSE"/>
+            <param name="correct" value="TRUE"/>
+            <output name="output_file" file="two_sided_two_columns_test_output.txt"/>
+        </test>
     </tests>
 
     <help><![CDATA[
-        **What it does**
+**What it does**
 
-        This tool compute a Wilcoxon test with R's wilcox.test function.
-
+This tool compute a Wilcoxon test with R's wilcox.test function.
     ]]></help>
 
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
--- a/test-data/input_file.txt	Thu Apr 14 10:37:32 2016 -0400
+++ b/test-data/input_file.txt	Thu Apr 21 04:20:40 2016 -0400
@@ -1,219 +1,45 @@
-1CMET2-PWY	0.175035	0.0362591
-ALLANTOINDEG-PWY	0.0242562	0.00460458
-ANAEROFRUCAT-PWY	0.217334	0.0455255
-ANAGLYCOLYSIS-PWY	0.281499	0.0629425
-ARGDEG-PWY	0.0596968	0.0103622
-ARGININE-SYN4-PWY	0.0573312	0.0491229
-ARGORNPROST-PWY	0.242842	0.0422785
-ARG+POLYAMINE-SYN	0.0310286	0.00566196
-ARGSYNBSUB-PWY	0.317406	0.0581645
-ARGSYN-PWY	0.386519	0.0687025
-ARO-PWY	0.230647	0.026966
-ASPASN-PWY	0.0946122	0.0522461
-AST-PWY	0.0287623	0.00643
-BIOTIN-BIOSYNTHESIS-PWY	0.0973993	0.0199678
-BRANCHED-CHAIN-AA-SYN-PWY	0.512372	0.167303
-CALVIN-PWY	0.278484	0.0422659
-CATECHOL-ORTHO-CLEAVAGE-PWY	0.00119794	0.0366668
-CENTFERM-PWY	0.00776542	0.0139536
-CHLOROPHYLL-SYN	0.0375381	0.00250693
-CITRULBIO-PWY	0.268125	0.028277
-COA-PWY	0.225052	0.0916386
-COA-PWY-1	0.246362	0.0829658
-COBALSYN-PWY	0.0303	0.00178244
-COLANSYN-PWY	0.0302351	0.0034277
-COMPLETE-ARO-PWY	0.240531	0.0289006
-CRNFORCAT-PWY	0.0506292	0.0121435
-DAPLYSINESYN-PWY	0.195661	0.0317622
-DENITRIFICATION-PWY	0.0083252	0.00290447
-DENOVOPURINE2-PWY	0.153298	0.0218334
-DTDPRHAMSYN-PWY	0.351623	0.0510527
-ECASYN-PWY	0.0262674	0.00376655
-ENTBACSYN-PWY	0.034469	0.00996603
-FAO-PWY	0.283098	0.681595
-FASYN-ELONG-PWY	0.509437	0.0906596
-FASYN-INITIAL-PWY	0.323496	0.0613045
-FERMENTATION-PWY	0.081389	0.0146486
-FUCCAT-PWY	0.0258997	0.0114288
-FUC-RHAMCAT-PWY	0.0214779	0.00269629
-GALACTARDEG-PWY	0.0535166	0.00630239
-GALACT-GLUCUROCAT-PWY	0.0246933	0.0029519
-GALACTUROCAT-PWY	0.0384389	0.013608
-GLCMANNANAUT-PWY	0.112131	0.0097333
-GLUCARDEG-PWY	0.0620383	0.00749099
-GLUCARGALACTSUPER-PWY	0.0535166	0.00630239
-GLUCONEO-PWY	0.251989	0.0401254
-GLUCOSE1PMETAB-PWY	0.201837	0.0252353
-GLUCUROCAT-PWY	0.0328287	0.0120152
-GLUDEG-I-PWY	0.0800248	0.051885
-GLUTORN-PWY	0.274208	0.0524521
-GLYCOCAT-PWY	0.0330107	0.00189397
-GLYCOGENSYNTH-PWY	0.126287	0.0497071
-GLYCOL-GLYOXDEG-PWY	0.0732694	0.0106957
-GLYCOLYSIS	0.196687	0.0477873
-GLYCOLYSIS-E-D	0.0315484	0.00558131
-GLYCOLYSIS-TCA-GLYOX-BYPASS	0.0396454	0.00485651
-GLYOXYLATE-BYPASS	0.0885671	0.0524551
-GOLPDLCAT-PWY	0.0434783	0.0148638
-HEME-BIOSYNTHESIS-II	0.3219	0.0975209
-HEMESYN2-PWY	0.336731	0.109504
-HEXITOLDEGSUPER-PWY	0.0397936	0.00830622
-HISDEG-PWY	0.102668	0.0612319
-HISTSYN-PWY	0.109704	0.0300389
-HOMOSER-METSYN-PWY	0.235047	0.0570343
-HSERMETANA-PWY	0.434001	0.124044
-ILEUSYN-PWY	0.548213	0.210067
-KDO-NAGLIPASYN-PWY	0.0123666	0.00293158
-KETOGLUCONMET-PWY	0.0616206	0.00888988
-LACTOSECAT-PWY	0.419374	0.0892027
-LEU-DEG2-PWY	0.0511478	0.0728135
-LPSSYN-PWY	0.0185716	0.00362221
-METHANOGENESIS-PWY	0.0352711	0.00632509
-METHGLYUT-PWY	0.231264	0.0358341
-MET-SAM-PWY	0.165071	0.0322526
-METSYN-PWY	0.185879	0.0402475
-NAD-BIOSYNTHESIS-II	0.0539411	0.0498032
-NAGLIPASYN-PWY	0.0282235	0.00548584
-NONMEVIPP-PWY	0.0366808	0.00468516
-NONOXIPENT-PWY	0.333471	0.119833
-OANTIGEN-PWY	0.064821	0.0115185
-ORNARGDEG-PWY	0.0596968	0.0103622
-ORNDEG-PWY	0.101108	0.0259131
-P105-PWY	0.0587574	0.00991824
-P122-PWY	0.0986031	0.0184304
-P125-PWY	0.478315	0.170173
-P161-PWY	0.229446	0.115246
-P185-PWY	0.25136	0.0335101
-P221-PWY	0.144829	0.0921912
-P241-PWY	0.0254264	0.00454012
-P261-PWY	0.0184375	0.00172471
-P42-PWY	0.265023	0.0654898
-P441-PWY	0.0380878	0.00589089
-P461-PWY	0.151406	0.0393084
-P562-PWY	0.00411946	0.00819304
-PANTO-PWY	0.256329	0.0475521
-PANTOSYN-PWY	0.18209	0.0156617
-PENTOSE-P-PWY	0.205923	0.0327824
-PEPTIDOGLYCANSYN-PWY	0.262078	0.0530054
-PHOSLIPSYN-PWY	0.0375214	0.00488223
-POLYAMSYN-PWY	0.0381404	0.00632617
-POLYISOPRENSYN-PWY	0.286387	0.0868964
-PPGPPMET-PWY	0.233335	0.12058
-PROTOCATECHUATE-ORTHO-CLEAVAGE-PWY	0.00243411	0.0782091
-PWY0-1061	0.156736	0.04166
-PWY0-1241	0.0202085	0.00392304
-PWY0-1261	0.0415094	0.00541882
-PWY0-1296	0.399844	0.0675016
-PWY0-1297	0.191777	0.0357239
-PWY0-1298	0.163573	0.0289767
-PWY0-1319	0.267442	0.0656443
-PWY0-1338	0.0203426	0.00423508
-PWY0-1415	0.185022	0.0203901
-PWY0-1479	0.00637332	0.000828996
-PWY0-1533	0.0380427	0.00285838
-PWY0-1586	0.642168	0.196749
-PWY0-162	0.272231	0.0299502
-PWY0-166	0.0333389	0.00866549
-PWY0-321	0.02807	0.00191978
-PWY0-41	0.022293	0.00457284
-PWY0-42	0.0263233	0.00457259
-PWY0-845	0.0281231	0.00723673
-PWY0-862	0.274273	0.074073
-PWY0-881	0.130657	0.0228336
-PWY-1042	0.546178	0.0910179
-PWY-1269	0.0356984	0.0466622
-PWY-1541	0.0107003	0.00398528
-PWY-181	0.00299148	0.00753257
-PWY-1861	0.193341	0.0236562
-PWY1F-823	0.0326328	0.0163749
-PWY-2941	0.227946	0.0506584
-PWY-2942	0.201976	0.0434436
-PWY-3001	0.431067	0.14867
-PWY-3661	0.0216369	0.00296086
-PWY-3781	1.01665	0.843165
-PWY-3801	0.0800445	0.0099032
-PWY-3841	0.234668	0.0438561
-PWY-3941	0.00804419	0.00163538
-PWY3O-355	0.205026	0.0418821
-PWY-4041	0.0983473	0.0101958
-PWY-4202	0.016321	0.00325086
-PWY-4242	0.161524	0.0226042
-PWY-4321	0.0526335	0.00770928
-PWY-4702	0.0482258	0.00779787
-PWY490-3	0.00130647	0.200701
-PWY-4981	0.282011	0.0412857
-PWY-4984	0.171295	0.024829
-PWY4FS-7	0.0819723	0.0120107
-PWY4FS-8	0.0819723	0.0120107
-PWY4LZ-257	0.150596	0.0469216
-PWY-5005	0.110835	0.0374559
-PWY-5022	0.151743	0.0736761
-PWY-5028	0.00383876	0.00105484
-PWY-5044	0.0521479	0.00482849
-PWY-5067	0.0455141	0.00375252
-PWY-5083	0.12172	0.060874
-PWY-5097	0.203122	0.0597759
-PWY-5100	0.447173	0.114717
-PWY-5101	0.103559	0.0397
-PWY-5103	0.473875	0.148779
-PWY-5104	0.41219	0.0707721
-PWY-5121	0.037774	0.00606188
-PWY-5136	0.259713	0.559791
-PWY-5138	0.176534	0.487365
-PWY-5154	0.0968213	0.0197088
-PWY-5173	0.736598	0.208526
-PWY-5177	0.0081314	0.156677
-PWY-5188	0.224444	0.0615877
-PWY-5189	0.220234	0.0814457
-PWY-5198	0.016533	0.00830795
-PWY-5265	0.263505	0.0417052
-PWY-5345	0.188272	0.0388054
-PWY-5347	0.208183	0.0452868
-PWY-5367	0.00470335	0.00407643
-PWY-5384	0.0694129	0.0127544
-PWY-5484	0.201531	0.048253
-PWY-5505	0.122036	0.104077
-PWY-5531	0.0366897	0.00246808
-PWY-5656	0.0189327	0.00442865
-PWY-5659	0.28852	0.434109
-PWY-5667	0.267442	0.0656443
-PWY-5675	0.0435654	0.109824
-PWY-5676	0.186911	0.143976
-PWY-5686	0.354435	0.0575302
-PWY-5690	0.370623	0.0588303
-PWY-5692	0.02766	0.00401055
-PWY-5695	0.601184	0.462119
-PWY-5705	0.0254948	0.00490674
-PWY-5723	0.133117	0.0159298
-PWY-5747	0.0135783	0.00457259
-PWY-5791	0.168964	0.0222139
-PWY-5837	0.168964	0.0222139
-PWY-5838	0.0300926	0.00455528
-PWY-5840	0.162422	0.0187953
-PWY-5855	0.0817978	0.0152219
-PWY-5856	0.028519	0.00420931
-PWY-5857	0.0817978	0.0152219
-PWY-5861	0.0275695	0.0035595
-PWY-5863	0.179896	0.0239585
-PWY-5897	0.1599	0.0182945
-PWY-5898	0.1599	0.0182945
-PWY-5899	0.1599	0.0182945
-PWY-5910	0.252076	0.039609
-PWY-5913	0.0489618	0.0648256
-PWY-5918	0.196254	0.0240698
-PWY-5920	0.161464	0.0152855
-PWY-5973	0.288863	0.0722322
-PWY-5989	0.250933	0.0530738
-PWY-5994	0.0482267	0.00511879
-PWY-6071	0.025905	0.00177062
-PWY-6121	0.330102	0.131432
-PWY-6122	0.336066	0.147505
-PWY-6123	0.177727	0.0374826
-PWY-6124	0.197165	0.0785672
-PWY-6125	0.182839	0.0190162
-PWY-6126	0.319041	0.0467433
-PWY-6147	0.0160686	0.0260844
-PWY-6151	0.255935	0.0425932
-PWY-6163	0.262483	0.0259363
-PWY-6168	0.144164	0.0339279
-PWY-6185	0.00480651	0.00207427
\ No newline at end of file
+GO:0000160	phosphorelay signal transduction system	2.24188560912	0.728693934232	2.27727933683	0.749521959908
+GO:0000746	conjugation	0.0994837099605	0.041803266954	0.0153440543392	0.0123485894543
+GO:0000902	cell morphogenesis	8.11126977702e-06	0.0501066555955	4.12343924065e-05	0.0426587635694
+GO:0002376	immune system process	0.085489980287	0.0	0.0275218309404	0.00149679872174
+GO:0005975	carbohydrate metabolic process	3.93695964707	3.53466664758	3.82956086917	4.33023870198
+GO:0006091	generation of precursor metabolites and energy	1.07156623777	1.0906071495	1.17950701314	1.06085609403
+GO:0006259	DNA metabolic process	7.83088558928	5.06907560378	7.58396051319	4.27934754543
+GO:0006412	translation	4.20183364466	2.74183619419	5.03906963774	3.04486279969
+GO:0006520	cellular amino acid metabolic process	6.18101744575	3.82270833632	6.27139841544	3.78690076599
+GO:0006629	lipid metabolic process	2.22295409952	0.98294942091	2.54389716799	1.18920658442
+GO:0006790	sulfur compound metabolic process	1.45678041362	0.428626648151	1.37494525671	0.342766907277
+GO:0006807	nitrogen compound metabolic process	6.29928644413	17.1144292852	6.08311422603	15.9266867986
+GO:0006810	transport	4.61323317367	8.81648079483	3.18084754012	8.87713901893
+GO:0006811	ion transport	2.84530948465	1.81185666634	2.90259750702	1.89008258587
+GO:0006935	chemotaxis	0.00293746066557	0.132567894519	0.0120376618448	0.0841949280975
+GO:0006950	response to stress	1.94565920911	1.44736653735	2.0733055949	1.4305653783
+GO:0007154	cell communication	0.721015903582	1.15674793488	0.709743568009	1.18696138634
+GO:0007165	signal transduction	0.118779041384	1.12181643785	0.0745544227737	1.16488360519
+GO:0009056	catabolic process	2.8187943392	1.45624257348	2.98058889328	1.56752246133
+GO:0009058	biosynthetic process	19.0004196424	14.2414568152	19.1704185155	13.7907550227
+GO:0009117	nucleotide metabolic process	3.44391451912	1.42846917009	3.70529753166	1.38640981601
+GO:0009306	protein secretion	0.0636027918464	0.176375427696	0.0756710986973	0.150802471215
+GO:0009404	toxin metabolic process	0.03091092162	0.014316187313	0.0362106070805	0.0130969888151
+GO:0009405	pathogenesis	1.43460861083	0.541438204177	0.368367078771	0.122737495182
+GO:0015979	photosynthesis	0.232009822868	0.0798843252065	0.167653248687	0.0703495399215
+GO:0016032	viral process	0.00123963164065	0.0128845685817	0.00242960292976	0.0134711884956
+GO:0016043	cellular component organization	2.24641451781	0.697770969635	2.38025522473	0.654101041398
+GO:0016049	cell growth	0.000155245877721	0.0	0.0420673650671	0.0
+GO:0016070	RNA metabolic process	2.37121554921	5.80206439421	2.38215565603	5.74546189338
+GO:0016310	phosphorylation	2.50223255226	0.848090936421	1.9906050825	0.866646459884
+GO:0019538	protein metabolic process	2.25811799055	5.09713533092	1.9377105334	5.82741162339
+GO:0022900	electron transport chain	0.3062712212	0.360767920287	0.237876158003	0.278030362562
+GO:0030031	cell projection assembly	0.0642099836606	0.0355041445362	0.0413581109156	0.0142195878565
+GO:0032196	transposition	0.722175839172	0.299208314842	2.633467426	0.919782814506
+GO:0042592	homeostatic process	0.991966070514	0.362485862765	0.715433785162	0.325553721977
+GO:0043934	sporulation	0.0768001451434	0.0160341297906	0.0916709924953	0.00673559424781
+GO:0044281	small molecule metabolic process	6.91812462508	7.90797554796	7.74857313252	8.04978352548
+GO:0045333	cellular respiration	0.338287752671	0.686031696039	0.175606167551	0.522008554205
+GO:0046034	ATP metabolic process	1.36885696133	0.377661021316	1.37948961282	0.321811725173
+GO:0048870	cell motility	0.322410195844	0.136003779473	0.153352240024	0.0722205383237
+GO:0051186	cofactor metabolic process	4.61150014233	1.60312665531	4.55766657384	1.41821678885
+GO:0051301	cell division	1.32835952519	0.120828620922	1.26384039624	0.0942983194692
+GO:0055114	oxidation-reduction process	0.131832728405	7.08823066241	0.300772862677	7.94837541209
+GO:0071554	cell wall organization or biogenesis	0.00369855395882	0.456400051538	0.0153325835178	0.403387255508
+GO:0071941	nitrogen cycle metabolic process	0.5367849148	0.0612732816996	0.267403669367	0.0160905862586
--- a/test-data/output_file.txt	Thu Apr 14 10:37:32 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-statistic	22435
-parameter	parameter
-p.value	2.0527634209064e-29
-null.value	0
-alternative	two.sided
-method	Wilcoxon signed rank test with continuity correction
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_sided_two_columns_test_output.txt	Thu Apr 21 04:20:40 2016 -0400
@@ -0,0 +1,6 @@
+statistic	981
+parameter	parameter
+p.value	0.916918193979449
+null.value	0
+alternative	two.sided
+method	Wilcoxon rank sum test with continuity correction