proteore_topgo: topGO.xml comparison

comparison topGO.xml @ 13:aba2aa04c7aa draft

planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72

author	proteore
date	Fri, 27 Sep 2019 05:49:07 -0400
parents	8eaa43ba1bfc
children	35fc495473ec

comparison

equal deleted inserted replaced

-:8eaa43ba1bfc
+:aba2aa04c7aa
-<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.27">
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.09.26">
 <description>(Human, Mouse, Rat)[topGO]</description>
 <requirements>
-<requirement type="package" version="3.4.1">R</requirement>
+<requirement type="package">R</requirement>
-<requirement type="package" version="3.0.0">r-ggplot2</requirement>
+<requirement type="package">r-ggplot2</requirement>
-<requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
+<requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
-<requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
+<requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
-<requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement>
+<requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement>
 <!--requirement type="package" version="3.6.0">bioconductor-org.ce.eg.db</requirement-->
 <!--requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement-->
 <!--requirement type="package" version="3.6.0">bioconductor-org.sc.sgd.db</requirement-->
 <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement-->
-<requirement type="package" version="1.56.0">bioconductor-graph</requirement>
+<requirement type="package" version="1.62.0">bioconductor-graph</requirement>
-<requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
+<requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement>
-<requirement type="package" version="3.5.0">bioconductor-go.db</requirement>
+<requirement type="package" version="3.8.2">bioconductor-go.db</requirement>
-<requirement type="package" version="2.30.0">bioconductor-topgo</requirement>
+<requirement type="package" version="2.36.0">bioconductor-topgo</requirement>
 </requirements>
 <stdio>
 <exit_code range="1:" />
 </stdio>
 <command><![CDATA[
 Rscript --vanilla $__tool_directory__/topGO_enrichment.R
 --inputtype="$inputtype.filetype"
 --input='$inputtype.genelist'
 #if $inputtype.filetype == "file"
 --column='$inputtype.column'
 --option='$option'
 --threshold='$threshold'
 --correction='$correction'
 --textoutput='true'
 --plot='$plot'
 --geneuniverse='$geneuniverse'
 --background="$background_genes.background"
 #if $background_genes.background == "true"
 --background_genes="$background_genes.inputtype.genelist"
 --background_input_type="$background_genes.inputtype.filetype"
 <inputs>
 <conditional name="inputtype">
 <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>
 <when value="copy_paste">
 <param name="genelist" type="text" label="Enter a list of IDs">
 <sanitizer>
 <valid initial="string.printable">
 </param>
 </when>
 <when value="file">
 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
 <param name="column" type="text" label="Column number of IDs" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on">
 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
 </param>
 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
 </when>
 </conditional>
 <conditional name="background_genes">
 <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)">
 <option value="file" selected="true">Input file containing your background IDs</option>
 <option value="copy_paste">Copy/paste your background IDs</option>
 </param>
 <when value="copy_paste">
 <param name="genelist" type="text" label="Copy/paste your background IDs" help="IDs must be separated by spaces into the form field, for example: ENSG00000139618 ENSG00000007350">
 <sanitizer>
 <valid initial="string.printable">
 </sanitizer>
 </param>
 </when>
 <when value="file">
 <param name="genelist" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help=""/>
 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header ?" />
 <param name="column" type="text" label="Column number of IDs" value="c1" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on">
 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
 </param>
 </when>
 </conditional>
 </when>
 <when value="false"/>
 </conditional>
 </data>
 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
 <filter>'barplot' in plot</filter>
 </data>
 </outputs>
 <tests>
 <test>
 <conditional name="inputtype">
 <param name="filetype " value="tabfile"/>
 <param name="header" value="TRUE"/>
 </conditional>
 <param name="ontocat" value="BP"/>
 <param name="option" value="elim"/>
 <param name="threshold" value="1e-3"/>
 <param name="correction" value="BH"/>
 <param name="textoutput" value="TRUE"/>
 <param name="plot" value="dotplot,barplot"/>
 <param name="geneuniverse" value="org.Hs.eg.db"/>
 <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[
 **Description**
 This tool is based on R package topGO. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be applied.
 This component computes the GO terms representativity of a gene list in one ontology category (Biological Process "BP", Cellular Component "CC", Molecular Function "MF"). This representativity is evaluated in comparison to the background list of all genes/proteins (of the selected species) associated associated with GO terms of the chosen category (BP,CC,MF).
 -----
 **Input required**
 This component works with Ensembl gene IDs (e.g : ENSG0000013618). You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
 and then specifying the column number that contains the ENSG IDs.
 -----
 **Parameters**
 "Species": "Species": the three available species are Homo sapiens, Mus musculus and Rattus norvegicus
 "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF)
 "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)
 "Multiple testing procedure (p-value adjustment): several FDR procedure for multiple testing and p-value adjustment are available: Holm, Hochberg
 -----
 **Output**
 Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)).
 *Textual output*
 The text output lists all the GO-terms that were found significantly enriched according to the specified threshold (p-value).
 The different fields are as follow:
 - Annotated : number of genes in the selected species that are annotated with the GO-term.
 - Significant : number of genes belonging to your input annotated with the GO-term.
 - Expected : represents the expected number of interesting genes mapped to the GO term if the interesting genes were randomly distributed over all GO terms.
 - p-values : p-value obtained after the test
 - ( q-values  : additional column with adjusted pvalues )
 -----
 .. class:: infomark
 Packages used:
-- bioconductor-org.hs.eg.db v3.5.0
+- bioconductor-org.hs.eg.db v3.8.2
-- bioconductor-org.mm.eg.db v3.5.0
+- bioconductor-org.mm.eg.db v3.8.2
-- bioconductor-org.rn.eg.db v3.5.0
+- bioconductor-org.rn.eg.db v3.8.2
-- bioconductor-annotationdbi v1.40.0
+- bioconductor-annotationdbi v1.46.0
-- bioconductor-go.db v3.5.0
+- bioconductor-go.db v3.8.2
-- bioconductor-graph v1.56.0
+- bioconductor-graph v1.62.0
-- bioconductor-topgo v2.30.0
+- bioconductor-topgo v2.36.0
 -----
 .. class:: infomark

Mercurial > repos > proteore > proteore_topgo

comparison topGO.xml @ 13:aba2aa04c7aa draft