# HG changeset patch
# User proteore
# Date 1561713500 14400
# Node ID 8eaa43ba1bfc30bd063bb0df913a25ec98a7515e
# Parent  fa2e27165d5d329269a9a0619a0e73b46c951eb7
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty

diff -r fa2e27165d5d -r 8eaa43ba1bfc README.rst
--- a/README.rst	Mon Mar 04 08:37:49 2019 -0500
+++ b/README.rst	Fri Jun 28 05:18:20 2019 -0400
@@ -66,3 +66,12 @@
 - BH
 - BY
 - fdr
+
+**Packages used**
+    - bioconductor-org.hs.eg.db v3.5.0
+    - bioconductor-org.mm.eg.db v3.5.0
+    - bioconductor-org.rn.eg.db v3.5.0
+    - bioconductor-annotationdbi v1.40.0
+    - bioconductor-go.db v3.5.0
+    - bioconductor-graph v1.56.0
+    - bioconductor-topgo v2.30.0
\ No newline at end of file
diff -r fa2e27165d5d -r 8eaa43ba1bfc test-data/Barplot_output_for_topGO_analysis_BP_category.png
Binary file test-data/Barplot_output_for_topGO_analysis_BP_category.png has changed
diff -r fa2e27165d5d -r 8eaa43ba1bfc test-data/Dotplot_output_for_topGO_analysis_BP_category.png
Binary file test-data/Dotplot_output_for_topGO_analysis_BP_category.png has changed
diff -r fa2e27165d5d -r 8eaa43ba1bfc test-data/Text_output_for_topGO_analysis_BP_category.tabular
--- a/test-data/Text_output_for_topGO_analysis_BP_category.tabular	Mon Mar 04 08:37:49 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-GO.ID	Term	Annotated	Significant	Expected	pvalues	qvalues
-GO:0070268	cornification	125	19	0.85	1.3e-20	1.007175e-16
-GO:0001895	retina homeostasis	72	13	0.49	1.9e-15	9.8135e-12
-GO:0010951	negative regulation of endopeptidase act...	253	19	1.72	8.7e-15	3.3701625e-11
-GO:0061621	canonical glycolysis	28	7	0.19	6.1e-10	1.89039e-06
-GO:0018149	peptide cross-linking	60	7	0.41	1.7e-07	0.000420578571428571
-GO:0061436	establishment of skin barrier	20	5	0.14	1.9e-07	0.000420578571428571
-GO:0042542	response to hydrogen peroxide	127	11	0.87	4.1e-07	0.00079411875
-GO:0002576	platelet degranulation	142	9	0.97	5.6e-07	0.000964133333333333
-GO:0098869	cellular oxidant detoxification	112	8	0.76	9.8e-07	0.00151851
-GO:0006094	gluconeogenesis	82	7	0.56	1.4e-06	0.00197209090909091
-GO:0001580	detection of chemical stimulus involved ...	55	6	0.37	2.0e-06	0.0025825
-GO:0007568	aging	297	11	2.02	6.1e-06	0.00727073076923077
-GO:0042744	hydrogen peroxide catabolic process	23	4	0.16	1.6e-05	0.017561
-GO:0045104	intermediate filament cytoskeleton organ...	47	5	0.32	1.7e-05	0.017561
-GO:0002934	desmosome organization	10	3	0.07	3.6e-05	0.03486375
-GO:0042493	response to drug	434	12	2.96	4.2e-05	0.0375142105263158
-GO:0045471	response to ethanol	138	7	0.94	4.5e-05	0.0375142105263158
-GO:0061740	protein targeting to lysosome involved i...	2	2	0.01	4.6e-05	0.0375142105263158
-GO:0070527	platelet aggregation	61	5	0.42	6.0e-05	0.046485
-GO:0046686	response to cadmium ion	64	5	0.44	7.5e-05	0.0553392857142857
-GO:0046718	viral entry into host cell	154	7	1.05	9.0e-05	0.0633886363636364
-GO:0043163	cell envelope organization	3	2	0.02	0.00014	0.0943173913043478
-GO:0070301	cellular response to hydrogen peroxide	83	5	0.57	0.00026	0.166869230769231
-GO:1903923	positive regulation of protein processin...	4	2	0.03	0.00027	0.166869230769231
-GO:0046716	muscle cell cellular homeostasis	19	3	0.13	0.00028	0.166869230769231
-GO:0051016	barbed-end actin filament capping	21	3	0.14	0.00038	0.218077777777778
-GO:0033591	response to L-ascorbic acid	5	2	0.03	0.00045	0.249026785714286
-GO:0019730	antimicrobial humoral response	95	5	0.65	0.00048	0.256468965517241
-GO:0006953	acute-phase response	56	4	0.38	0.00057	0.294405
-GO:0086073	bundle of His cell-Purkinje myocyte adhe...	6	2	0.04	0.00068	0.32926875
-GO:0071638	negative regulation of monocyte chemotac...	6	2	0.04	0.00068	0.32926875
-GO:0031069	hair follicle morphogenesis	27	3	0.18	0.00080	0.375636363636364
-GO:0048102	autophagic cell death	7	2	0.05	0.00095	0.408895833333333
-GO:0009635	response to herbicide	7	2	0.05	0.00095	0.408895833333333
-GO:0044829	positive regulation by host of viral gen...	7	2	0.05	0.00095	0.408895833333333
diff -r fa2e27165d5d -r 8eaa43ba1bfc test-data/barplot.png
Binary file test-data/barplot.png has changed
diff -r fa2e27165d5d -r 8eaa43ba1bfc test-data/dotplot.png
Binary file test-data/dotplot.png has changed
diff -r fa2e27165d5d -r 8eaa43ba1bfc test-data/result.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result.tsv	Fri Jun 28 05:18:20 2019 -0400
@@ -0,0 +1,63 @@
+GO.ID	Term	Annotated	Significant	Expected	pvalues	qvalues
+GO:0070268	cornification	128	21	1.01	4.8e-22	3.792e-18
+GO:0001895	retina homeostasis	70	15	0.55	6.8e-18	3.58133333333333e-14
+GO:0010951	negative regulation of endopeptidase act...	279	22	2.2	2.2e-11	8.69e-08
+GO:0061621	canonical glycolysis	27	7	0.21	1.3e-09	4.108e-06
+GO:0046718	viral entry into host cell	155	12	1.22	3.6e-09	9.48e-06
+GO:0042026	protein refolding	36	7	0.28	1.1e-08	2.054e-05
+GO:0002576	platelet degranulation	138	11	1.09	1.2e-08	2.054e-05
+GO:0070370	cellular heat acclimation	11	5	0.09	1.3e-08	2.054e-05
+GO:0070434	positive regulation of nucleotide-bindin...	11	5	0.09	1.3e-08	2.054e-05
+GO:0090063	positive regulation of microtubule nucle...	12	5	0.09	2.1e-08	3.01636363636364e-05
+GO:1900034	regulation of cellular response to heat	93	9	0.73	5.0e-08	6.58333333333333e-05
+GO:1903265	positive regulation of tumor necrosis fa...	16	5	0.13	1.2e-07	0.000145846153846154
+GO:0050821	protein stabilization	181	11	1.43	2.0e-07	0.000225714285714286
+GO:0090084	negative regulation of inclusion body as...	19	5	0.15	3.0e-07	0.000316
+GO:0061436	establishment of skin barrier	20	5	0.16	4.0e-07	0.000395
+GO:0018149	peptide cross-linking	60	7	0.47	4.4e-07	0.000408941176470588
+GO:0042542	response to hydrogen peroxide	136	11	1.07	1.0e-06	0.000877777777777778
+GO:1901673	regulation of mitotic spindle assembly	27	5	0.21	2.0e-06	0.00166315789473684
+GO:0098869	cellular oxidant detoxification	114	8	0.9	3.3e-06	0.002607
+GO:2000117	negative regulation of cysteine-type end...	116	8	0.91	3.8e-06	0.00285904761904762
+GO:0006094	gluconeogenesis	85	7	0.67	4.8e-06	0.00344727272727273
+GO:0034599	cellular response to oxidative stress	309	15	2.43	6.8e-06	0.00467130434782609
+GO:0001580	detection of chemical stimulus involved ...	61	6	0.48	8.4e-06	0.00553
+GO:0051092	positive regulation of NF-kappaB transcr...	173	9	1.36	9.5e-06	0.006004
+GO:0045104	intermediate filament cytoskeleton organ...	45	5	0.35	2.7e-05	0.0164076923076923
+GO:0042744	hydrogen peroxide catabolic process	23	4	0.18	2.9e-05	0.0169703703703704
+GO:0007568	aging	312	11	2.46	3.8e-05	0.0214428571428571
+GO:2001240	negative regulation of extrinsic apoptot...	49	5	0.39	4.1e-05	0.0223379310344828
+GO:0031397	negative regulation of protein ubiquitin...	172	10	1.35	4.7e-05	0.0247533333333333
+GO:0002934	desmosome organization	10	3	0.08	5.5e-05	0.0280322580645161
+GO:1902396	protein localization to bicellular tight...	2	2	0.02	6.2e-05	0.0296848484848485
+GO:1903923	positive regulation of protein processin...	2	2	0.02	6.2e-05	0.0296848484848485
+GO:0006953	acute-phase response	57	5	0.45	8.5e-05	0.0388228571428571
+GO:1900740	positive regulation of protein insertion...	30	4	0.24	8.6e-05	0.0388228571428571
+GO:0045471	response to ethanol	138	7	1.09	0.00011	0.0482777777777778
+GO:0070527	platelet aggregation	62	5	0.49	0.00013	0.0555135135135135
+GO:0032757	positive regulation of interleukin-8 pro...	63	5	0.5	0.00014	0.0567179487179487
+GO:0046686	response to cadmium ion	63	5	0.5	0.00014	0.0567179487179487
+GO:0003064	regulation of heart rate by hormone	3	2	0.02	0.00018	0.0677142857142857
+GO:0043163	cell envelope organization	3	2	0.02	0.00018	0.0677142857142857
+GO:0061740	protein targeting to lysosome involved i...	3	2	0.02	0.00018	0.0677142857142857
+GO:0042493	response to drug	438	12	3.45	0.00019	0.0698139534883721
+GO:0086091	regulation of heart rate by cardiac cond...	38	4	0.3	0.00022	0.079
+GO:0038061	NIK/NF-kappaB signaling	166	7	1.31	0.00035	0.121791666666667
+GO:0051016	barbed-end actin filament capping	18	3	0.14	0.00036	0.121791666666667
+GO:1902309	negative regulation of peptidyl-serine d...	4	2	0.03	0.00037	0.121791666666667
+GO:1905913	negative regulation of calcium ion expor...	4	2	0.03	0.00037	0.121791666666667
+GO:0010389	regulation of G2/M transition of mitotic...	226	8	1.78	0.00043	0.13865306122449
+GO:0043488	regulation of mRNA stability	174	7	1.37	0.00046	0.14536
+GO:0046716	muscle cell cellular homeostasis	20	3	0.16	0.00049	0.151803921568627
+GO:0006402	mRNA catabolic process	414	15	3.26	0.00050	0.151923076923077
+GO:0046827	positive regulation of protein export fr...	21	3	0.17	0.00057	0.169924528301887
+GO:0048549	positive regulation of pinocytosis	5	2	0.04	0.00061	0.172107142857143
+GO:0001907	killing by symbiont of host cells	5	2	0.04	0.00061	0.172107142857143
+GO:0033591	response to L-ascorbic acid	5	2	0.04	0.00061	0.172107142857143
+GO:0030216	keratinocyte differentiation	354	30	2.79	0.00065	0.180175438596491
+GO:0006754	ATP biosynthetic process	51	4	0.4	0.00069	0.187965517241379
+GO:0070301	cellular response to hydrogen peroxide	92	5	0.72	0.00080	0.214237288135593
+GO:0061844	antimicrobial humoral immune response me...	54	4	0.43	0.00086	0.226466666666667
+GO:0086073	bundle of His cell-Purkinje myocyte adhe...	6	2	0.05	0.00091	0.228222222222222
+GO:0032417	positive regulation of sodium:proton ant...	6	2	0.05	0.00091	0.228222222222222
+GO:0071638	negative regulation of monocyte chemotac...	6	2	0.05	0.00091	0.228222222222222
diff -r fa2e27165d5d -r 8eaa43ba1bfc topGO.xml
--- a/topGO.xml	Mon Mar 04 08:37:49 2019 -0500
+++ b/topGO.xml	Fri Jun 28 05:18:20 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.02.19">
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.27">
     <description>(Human, Mouse, Rat)[topGO]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -51,7 +51,7 @@
 
     <inputs>
   <conditional name="inputtype">
-    <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene only)" help="Copy/paste or from a file">
+    <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene Id)" help="Copy/paste or from a file">
       <option value="file" selected="true">Input file containing your IDs</option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
@@ -76,7 +76,7 @@
     </when>
   </conditional>
   <conditional name="background_genes">
-    <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/>
+    <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Use your own background (ID list) ?"/>
     <when value="true">
       <conditional name="inputtype">
         <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)">
@@ -106,7 +106,7 @@
     </when>
     <when value="false"/>
   </conditional>
-    <param name="geneuniverse" type="select" label="Species">
+    <param name="geneuniverse" type="select" label="Species (human, mouse, rat)">
       <!--option value="org.At.tair.db" >Arabidopsis</option-->
       <!--option value="org.Ce.eg.db" >Worm (C. elegans)</option-->
       <!--option value="org.Dm.eg.db" >Fly (D. melanogaster)</option-->
@@ -120,7 +120,7 @@
       <option value="CC" >Cellular Component</option>
       <option value="MF" >Molecular Function</option>
     </param>
-    <param name="option" type="select" label="Select the topGO parameter (see user doc)">
+    <param name="option" type="select" label="Select GO scoring method (read user doc section)">
       <option value="classic" >Classic Fisher test</option>
       <option value="elim" selected="true">Elim</option>
       <option value="weight01" >Weight01</option>
@@ -170,19 +170,12 @@
        <param name="option" value="elim"/>
        <param name="threshold" value="1e-3"/>
        <param name="correction" value="BH"/> 
-       <conditional name="condtext">
-         <param name="textoutput" value="TRUE"/>
-       </conditional>
-       <conditional name="condbar">
-         <param name="barplotoutput" value="TRUE"/>
-       </conditional>
-       <conditional name="conddot">
-         <param name="dotoutput" value="TRUE"/>
-       </conditional>
+       <param name="textoutput" value="TRUE"/>
+       <param name="plot" value="dotplot,barplot"/>
        <param name="geneuniverse" value="org.Hs.eg.db"/>
-       <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/>
-       <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/>
-       <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/>
+       <output name="outputtext" file="result.tsv"/>
+       <output name="outputbarplot" file="barplot.png" compare="sim_size"/>
+       <output name="outputdotplot" file="dotplot.png" compare="sim_size"/>
      </test>
    </tests>
    <help><![CDATA[
@@ -209,7 +202,7 @@
  
 "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF)
  
-"Select the topGO parameter (see user doc)": topGO provides a classic Fisher test for evaluating which GO terms are over-represented in your gene/protein list; other methodologies are also provided (Elim, Weight01, Parentchild). For the merits of each option and their algorithmic descriptions, please refer to topGO manual: 
+"Select GO scoring method: topGO provides the commonly used Fisher test for evaluating which GO terms are over-represented in your gene/protein list; it also provides other GO scoring algorithms (i.e. Elim, Weight01, Parentchild). For the merits of each option and their algorithmic description, please refer to topGO manual: 
 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
 
 "p-value threshold (e.g : 1e-3)": must be in the form of "1e-5" (i.e. 0.00001)
@@ -221,7 +214,7 @@
 
 **Output**
 
-Three outputs are available : a textual output, a barplot and/or a dotplot (set by default) graphical outputs. 
+Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)). 
 
 *Textual output*
 
@@ -243,6 +236,19 @@
 
 .. class:: infomark
 
+Packages used: 
+    - bioconductor-org.hs.eg.db v3.5.0
+    - bioconductor-org.mm.eg.db v3.5.0
+    - bioconductor-org.rn.eg.db v3.5.0
+    - bioconductor-annotationdbi v1.40.0
+    - bioconductor-go.db v3.5.0
+    - bioconductor-graph v1.56.0
+    - bioconductor-topgo v2.30.0
+
+-----
+
+.. class:: infomark
+
 **Authors**
 
 Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006. 22(13):1600-7. PubMed PMID: 16606683.
@@ -253,13 +259,13 @@
 
 **Galaxy integration**
 
-Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+Lisa Perus, 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, FR
 
 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
 
-Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+Help: contact@proteore.org for any questions or concerns about this tool.
 
 ]]></help>
    <citations>
diff -r fa2e27165d5d -r 8eaa43ba1bfc topGO_enrichment.R
--- a/topGO_enrichment.R	Mon Mar 04 08:37:49 2019 -0500
+++ b/topGO_enrichment.R	Fri Jun 28 05:18:20 2019 -0400
@@ -215,7 +215,7 @@
     return(c(NULL,NULL))
   }
   
-  geneList = factor(as.integer(allGenes %in% sample)) 
+  geneList = factor(as.integer(allGenes %in% sample)) #duplicated ids in sample count only for one
   if (length(levels(geneList)) == 1 ){
     stop("All or none of the background genes are found in tested genes dataset, enrichment analysis can't be done")
   }