Mercurial > repos > proteore > proteore_go_terms_enrich_comparison
view GO_terms_enrich_comparison.xml @ 1:528652235016 draft
planemo upload commit c9d70181a2b587e53dcc4b5885b74b625def6b8c-dirty
author | proteore |
---|---|
date | Fri, 13 Dec 2019 05:16:36 -0500 |
parents | 04f363ee805a |
children | ec6f7de49e86 |
line wrap: on
line source
<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2019.12.13"> <description>(Human, Mouse, Rat)[clusterProfiler]</description> <requirements> <requirement type="package">R</requirement> <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement> <requirement type="package" version="3.10.2">bioconductor-dose</requirement> <requirement type="package" version="3.12.0">bioconductor-clusterprofiler</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript $__tool_directory__/GO_terms_enrich_comparison.R --nb=$len($lists) #for $index, $list in enumerate($lists) #if $list.input.ids == "file" --input.$index="$list.input.file" --name.$index="$list.list_name" --inputtype.$index="file" --header.$index="$list.input.header" --column.$index="$list.input.ncol" #else --input.$index="$list.input.txt" --name.$index="$list.list_name" --inputtype.$index="text" #end if #end for --org="$species" --ont="$ontology" > $log ]]></command> <inputs> <repeat name="lists" title="List to compare" min="2" max="5" > <conditional name="input" > <param name="ids" type="select" label="Enter your Gene ID list" help="Copy/paste or from a file (e.g. table)" > <option value="text">Copy/paste your IDs</option> <option value="file" selected="true">Input file containing your IDs</option> </param> <when value="text" > <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: 2810 7534' > <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> </when> <when value="file" > <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> <param name="ncol" type="text" value="c1" 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> </when> </conditional> <param name="list_name" type="text" label="name of your list" value="list" optional="false"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator> </param> </repeat> <param name="species" type="select" label="Species" > <option value="org.Hs.eg.db">Human (Homo sapiens) </option> <option value="org.Mm.eg.db">Mouse (Mus musculus) </option> <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option> </param> <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" > <option value="CC">Cellular Component</option> <option value="BP">Biological Process</option> <option value="MF">Molecular Function</option> </param> </inputs> <outputs> <data name="log" format="txt" label="GO enrich comparison" /> <collection type="list" label="GO enrichComparison results Table" name="text_output"> <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/> </collection> <collection type="list" label="GO enrichComparison results Diagram" name="graph_output" > <discover_datasets pattern="(?P<designation>.+.png)" ext="png" /> </collection> </outputs> <tests> <test> <repeat name="lists"> <conditional name="input"> <param name="ids" value="file" /> <param name="file" value="Gene_ID_BreastUp.txt" /> <param name="header" value="true" /> <param name="ncol" value="c7" /> <param name="name" value="UP" /> </conditional> </repeat> <repeat name="lists"> <conditional name="input"> <param name="ids" value="file" /> <param name="file" value="Gene_ID_BreastDn.txt" /> <param name="header" value="true" /> <param name="ncol" value="c7" /> <param name="name" value="DN" /> </conditional> </repeat> <param name="species" value="org.Hs.eg.db"/> <param name="ontology" value="BP"/> <output name="log" file="log.txt" /> <output_collection name="text_output"> <element name="GO_enrich_comparison_BP.tsv" file="GO_enrich_comparison_BP.tsv" ftype="tsv"/> </output_collection> <output_collection name="graph_output"> <element name="GO_enrich_comparison_BP.png" file="GO_enrich_comparison_BP.png" ftype="png"/> </output_collection> </test> </tests> <help><![CDATA[ **Description** This tool is based on the R package clusterProfiler and allows to compare GO terms enrichment analyses of gene/protein sets. Given a list of gene set, this function will compute GO enrichment profiles of each gene list. This tool calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background. User has the possibility to use background corresponding to the whole organism or to a user-defined list. In this latter case, user has the possibility to use the "Build tissue-specific expression dataset" ProteoRE tool to create this list according to your need. ----- **Input** Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space). "Enter your Gene ID list": only Entrez Gene ID (e.g : 4151, 7412). If your IDs are not Entrez Gene IDs, please use the ID_Converter tool of ProteoRE. "Does file contain header?": in case of file input, you specify if there is header or not. "Column number of IDs": in which column are your IDs. (e.g. for column 2 you write "c2") "name of your list": write the name for this list ----- **Parameters** "Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus "Select GO terms category": allows you to perform analysis on one, two or three categories of the Gene Ontology. The categories are Cellular Component (CC), Biological Process (BP) and Molecular Function (MF). ----- **Output** Diagram output: graphical output in the form of a dot-plot (png, jpeg or pdf format), one figure for each GO category. Text tables: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)d graphics representing the repartition and/or enrichment of GO categories. One table and one graphic will be produced for each GO catagory. ----- **Authors** G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118) User manual / Documentation of the clusterProfiler R package (functions and parameters): https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html ----- .. class:: infomark **Galaxy integration** 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> <citations> </citations> </tool>