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changeset 1:e646ad125f2d draft

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Add test
author lecorguille
date Tue, 04 Aug 2015 09:46:07 -0400
parents 8dd2a438bfba
children b6298c38e53f
files abims_anova.xml static/images/anova_workflow.png static/images/hclust.png static/images/pca_abims_Rplots.png static/images/pca_abims_Rplots1.png static/images/pca_abims_eigenvalue.png static/images/pca_abims_percentage_of_variance.png test-data/dataMatrix.tsv test-data/dataMatrix.tsv_anova_filtered.tabular test-data/dataMatrix.tsv_anova_pvalue.tabular test-data/sampleMetadata.tsv
diffstat 11 files changed, 141 insertions(+), 63 deletions(-) [+]
line wrap: on
line diff
--- a/abims_anova.xml	Tue Jun 30 06:02:46 2015 -0400
+++ b/abims_anova.xml	Tue Aug 04 09:46:07 2015 -0400
@@ -1,14 +1,17 @@
-<tool id="abims_anova" name="Anova" version="1.1">
-	
-    <requirements>
-	<requirement type="binary">Rscript</requirement>
-	<requirement type="binary">batch</requirement>
-    </requirements>
+<tool id="abims_anova" name="Anova" version="1.1.3">
     
     <description>N-way anova. With ou Without interactions</description>
+    
+    <requirements>
+        <requirement type="binary">Rscript</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
 
     <command interpreter="Rscript">
-        abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" 
+abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" 
 condition "c('$condition_1'
 #for $i, $s in enumerate( $conditions )
 ,'${s.condition}'
@@ -21,58 +24,72 @@
         <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
         <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" />
         
-         <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true">
-		<label>Mode</label>
-		<option value="row">row</option>
-		<option value="column">column</option>
-	</param>
-	
-	<param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
-	<repeat name="conditions" title="Conditions for N-ways anova">
-	    <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
-	</repeat>
+        <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true">
+            <label>Mode</label>
+            <option value="row">row</option>
+            <option value="column">column</option>
+        </param>
+    
+        <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
+        <repeat name="conditions" title="Conditions for N-ways anova">
+            <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
+        </repeat>
 
-	<param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" />
-        
-	<param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" format="text" optional="true">
-		<label>PValue adjusted method</label>
-		<option value="BH">BH</option>
-		<option value="holm">holm</option>
-		<option value="bonferroni">bonferroni</option>
-		<option value="hochberg">hochberg</option>
-		<option value="hommel">hommel</option>
-		<option value="BY">BY</option>
-		<option value="fdr">fdr</option>
-		<option value="none">none</option>		
-	</param>        
+        <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" />
+            
+        <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" format="text" optional="true">
+            <label>PValue adjusted method</label>
+            <option value="BH">BH</option>
+            <option value="holm">holm</option>
+            <option value="bonferroni">bonferroni</option>
+            <option value="hochberg">hochberg</option>
+            <option value="hommel">hommel</option>
+            <option value="BY">BY</option>
+            <option value="fdr">fdr</option>
+            <option value="none">none</option>		
+        </param>        
         
         <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" />
 
         <param name="selection_method" type="select" format="text" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. ">
-		<label>Selection method</label>
-		<option value="intersection" selected="true">intersection / strong</option>
-		<option value="union">union / weak</option>
-	</param>
+            <label>Selection method</label>
+            <option value="intersection" selected="true">intersection / strong</option>
+            <option value="union">union / weak</option>
+        </param>
 
         <param name="sep" type="select" format="text">
-		<label>Separator of columns</label>
-		<option value="tabulation">tabulation</option>
-		<option value="semicolon">;</option>
-		<option value="comma">,</option>
-	</param>
+            <label>Separator of columns</label>
+            <option value="tabulation">tabulation</option>
+            <option value="semicolon">;</option>
+            <option value="comma">,</option>
+        </param>
         
         <param name="dec" type="text" label="Decimal separator" value="." help="" />
 
     </inputs>
 
     <outputs>
-        <data name="dataMatrixPValue" format="input" label="${input.name}_anova_pvalue.${input.ext}"/>
-        <data name="dataMatrixFiltered" format="input" label="${input.name}_anova_filtered.${input.ext}"/>
+        <data name="dataMatrixPValue" format_source="input" label="${input.name}_anova_pvalue.${input.ext}"/>
+        <data name="dataMatrixFiltered" format_source="input" label="${input.name}_anova_filtered.${input.ext}"/>
     </outputs>
-
-    <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>
+    
+    <tests>
+        <test>
+            <param name="input" value="dataMatrix.tsv"/>
+            <param name="sampleinfo" value="sampleMetadata.tsv"/>
+            <param name="mode" value="row"/>
+            <param name="condition_1" value="age"/>
+            <param name="conditions_0|condition" value="gender"/>
+            <param name="interaction" value="F"/>
+            <param name="method" value="BH"/>
+            <param name="threshold" value="0.05"/>
+            <param name="selection_method" value="union"/>
+            <param name="sep" value="tabulation"/>
+            <param name="dev" value="."/>
+            <output name="dataMatrixPValue" file="dataMatrix.tsv_anova_pvalue.tabular" />
+            <output name="dataMatrixFiltered" file="dataMatrix.tsv_anova_filtered.tabular" />
+        </test>
+    </tests>
 
     <help>
 
@@ -117,23 +134,23 @@
 
 ***.anova_pvalue.tabular**
 
-	| A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue).
+    | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue).
 
 ***.anova_filtered.tabular**
 
-	| The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue.
-	
-	
+    | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue.
+    
+    
 ------
 
 .. class:: infomark 
 
 The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools:
-	| PCA
-	| Hierarchical Clustering
+    | PCA
+    | Hierarchical Clustering
 
-	
-	
+    
+    
 ---------------------------------------------------
 
 ---------------
@@ -145,7 +162,7 @@
 -----------
 
 **>A part of an example of Data Matrix file input**
-	
+    
 
 +--------+------------------+----------------+
 | Name   | Bur-eH_FSP_12    | Bur-eH_FSP_24  |	                                       
@@ -156,8 +173,8 @@
 +--------+------------------+----------------+       
 
 **>A part of an example of Sample Metadata file input**
-	
-	
+    
+    
 +---------------------------+------------+------------+------------+
 | Sample name               |   class    |   time     |   batch    |
 +===========================+============+============+============+
@@ -173,13 +190,13 @@
 Parameters
 ----------
 
-	| Mode -> **row**
-	| column name of condition -> **class**
-	| Separator of columns: -> **tabulation**
-	| Decimal separator -> **.**
-	| PValue adjusted method -> **BH**
-	| Threshold -> **0.001**
-	
+    | Mode -> **row**
+    | column name of condition -> **class**
+    | Separator of columns: -> **tabulation**
+    | Decimal separator -> **.**
+    | PValue adjusted method -> **BH**
+    | Threshold -> **0.001**
+    
 
 
 Output files
@@ -194,6 +211,11 @@
 .. image:: anova_filtered.png
 
 
+
     </help>
 
+    <citations>
+        <citation>Ronald A. Fisher in the 1930s</citation>
+    </citations>
+
 </tool>
Binary file static/images/anova_workflow.png has changed
Binary file static/images/hclust.png has changed
Binary file static/images/pca_abims_Rplots.png has changed
Binary file static/images/pca_abims_Rplots1.png has changed
Binary file static/images/pca_abims_eigenvalue.png has changed
Binary file static/images/pca_abims_percentage_of_variance.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataMatrix.tsv	Tue Aug 04 09:46:07 2015 -0400
@@ -0,0 +1,16 @@
+dataMatrix	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
+HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907
+HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742
+HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315
+HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030
+HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010
+HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661
+HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775
+HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898
+HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831
+HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900
+HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276
+HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
+HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811
+HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
+HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataMatrix.tsv_anova_filtered.tabular	Tue Aug 04 09:46:07 2015 -0400
@@ -0,0 +1,3 @@
+	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
+HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
+HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataMatrix.tsv_anova_pvalue.tabular	Tue Aug 04 09:46:07 2015 -0400
@@ -0,0 +1,16 @@
+	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208	pvalueadjusted.BH.age	pvalueadjusted.BH.gender
+HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907	0.740856975457218	0.740856975457218
+HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742	0.347623051099051	0.234554902330543
+HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315	0.720303175717481	0.720303175717481
+HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030	0.252979062487671	0.517822514350462
+HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010	0.808532959173048	0.808532959173048
+HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661	0.329174238111018	0.329174238111018
+HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775	0.995859884733937	0.995859884733937
+HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898	0.15341384456659	0.15341384456659
+HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831	0.439012867631325	0.596200901535843
+HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900	0.814406453193777	0.814406453193777
+HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276	0.288354536353544	0.288354536353544
+HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044	0.659785284053633	0.00376251274734483
+HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811	0.646714644805001	0.646714644805001
+HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554	0.13976111393526	0.0491480895853803
+HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061	0.565910223149305	0.565910223149305
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata.tsv	Tue Aug 04 09:46:07 2015 -0400
@@ -0,0 +1,21 @@
+sampleMetadata	injectionOrder	mode	age	bmi	gender
+HU_017	2	pos	40-50	23.03	M
+HU_028	7	pos	40-50	23.92	F
+HU_034	9	pos	50-60	23.37	M
+HU_051	20	pos	20-30	23.23	F
+HU_060	24	pos	50-60	28.72	F
+HU_078	34	pos	40-50	25.18	M
+HU_091	42	pos	60-70	26.12	M
+HU_093	43	pos	50-60	21.71	M
+HU_099	46	pos	20-30	21.3	M
+HU_110	53	pos	50-60	20.9	F
+HU_130	63	pos	30-40	26.06	M
+HU_134	67	pos	40-50	22.89	M
+HU_138	68	pos	40-50	21.88	M
+HU_149	72	pos	30-40	19.49	F
+HU_152	75	pos	20-30	17.58	F
+HU_175	87	pos	30-40	21.26	F
+HU_178	88	pos	60-70	32.87	F
+HU_185	95	pos	40-50	21.09	F
+HU_204	104	pos	30-40	29.06	M
+HU_208	106	pos	20-30	18.61	F