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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rdavidwebservice commit b664316c8917dff50de40207c2b3104ed850b90b
author | iuc |
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date | Thu, 23 May 2019 13:44:50 -0400 |
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<tool id="rdavidwebservice" name="RDAVIDWebService" version="@TOOL_VERSION@"> <description> Run functional annotation using DAVID </description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-rdavidwebservice</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ cat '$script' && Rscript '$script' ]]></command> <configfiles> <configfile name="script"><![CDATA[ ## Setup R error handling to go to stderr options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) ## Unify locale settings loc <- Sys.setlocale("LC_MESSAGES", "C.UTF-8") ## Import libraries library(RDAVIDWebService) gene_list <- scan('$input1', what="character") gene_identifier_type <- '$identifier1' #if str('$__user_email__') != "": email <- '$__user_email__' #else: email <- 'galaxy_user@galaxy.org' #end if david <- DAVIDWebService(email=email, url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/") geneList <- addList(david, gene_list, idType=gene_identifier_type, listName="genelist", listType="Gene") #if str($background.background_selector) == "with_background": background_list <- scan('$background.input2', what="character") background_identifier_type <- '$background.identifier2' background <- addList(david, background_list, idType=background_identifier_type, listName="backgroundlist",listType="Background") #end if #if str($AnnotationCategories.setAnnotationCategories) == "Yes": annocategories <- c('$AnnotationCategories.Disease', '$AnnotationCategories.Functional_Categories', '$AnnotationCategories.Gene_Ontology', '$AnnotationCategories.General_Annotations', '$AnnotationCategories.Literature', '$AnnotationCategories.Main_Accessions', '$AnnotationCategories.Pathways', '$AnnotationCategories.Protein_Domains', '$AnnotationCategories.Tissue_Expression') annocategories <- annocategories[annocategories != 'None'] annocategories <- unlist(strsplit(annocategories, split = ",")) setAnnotationCategories(david, annocategories) #end if #if str($FunctionalAnnotationCluster.set_FACluster_params) == "Yes": getClusterReportFile(david, '$output1', kappa = as.integer('$FunctionalAnnotationCluster.kappa'), overlap = as.integer('$FunctionalAnnotationCluster.overlap'), initialSeed = as.integer('$FunctionalAnnotationCluster.initialSeed'), finalSeed = as.integer('$FunctionalAnnotationCluster.finalSeed'), linkage = as.double('$FunctionalAnnotationCluster.linkage')) #end if #if str($FunctionalAnnotationChart.set_FAChart_params) == "Yes" : getFunctionalAnnotationChartFile(david, '$output2', count = as.integer('$FunctionalAnnotationChart.count'), threshold = as.double('$FunctionalAnnotationChart.threshold')) #end if #if str($FunctionalAnnotationTable.set_FATable_params) == "Yes": getFunctionalAnnotationTableFile(david, '$output3') #end if #if str($GeneListReport.set_GLReport_params) == "Yes": getGeneListReportFile(david, '$output4') #end if ]]></configfile> </configfiles> <inputs> <param name="input1" type="data" format="txt" label="Select gene list"/> <param name="identifier1" type="select" label="Select gene list identifier type"> <expand macro="identifier_options" /> </param> <param name="email" type="text" label="I acknowledge that this services will send my galaxy_user email address to an external service: DAVIDWebService. Please confirm with 'yes'." help="E-Mail has to be registered at https://david.ncifcrf.gov/webservice/register.htm in order to get access to DAVID (webservice)"> <validator type="regex" message="You need to agree the terms to continue by typing 'yes'">^'*[Yy]es'*$</validator> </param> <conditional name="background"> <param name="background_selector" type="select" label="Background" help="Default: entire species as background"> <option value="without_background">Use default Background</option> <option value="with_background">Use specify Background</option> </param> <when value="with_background"> <param name="input2" type="data" format="txt" label="Select gene list for background"/> <param name="identifier2" type="select" label="Select background list identifier type"> <expand macro="identifier_options" /> </param> </when> <when value="without_background"> </when> </conditional> <conditional name="AnnotationCategories"> <param name="setAnnotationCategories" type="select" label="Annotation Categories" help="Default: OMIM_DISEASE, COG_ONTOLOGY, UP_KEYWORDS, UP_SEQ_FEATURE, GOTERM_BP_DIRECT, GOTERM_MF_DIRECT, GOTERM_CC_DIRECT, BBID, BIOCARTA, KEGG_PATHWAY, INTERPRO, PIR_SUPERFAMILY, SMART"> <option value="without_AnnotationCategories">Use default Annotation Categories</option> <option value="with_AnnotationCategories">Use specify Annotation Categories</option> </param> <when value="with_AnnotationCategories"> <param name="Disease" type="select" display="checkboxes" multiple="true" label="Disease"> <option value="GAD_DISEASE">GAD_DISEASE</option> <option value="GAD_DISEASE_CLASS">GAD_DISEASE_CLASS</option> <option value="OMIM_DISEASE">OMIM_DISEASE</option> </param> <param name="Functional_Categories" type="select" display="checkboxes" multiple="true" label="Functional_Categories"> <option value="COG_ONTOLOGY">COG_ONTOLOGY</option> <option value="PIR_SEQ_FEATURE">PIR_SEQ_FEATURE</option> <option value="SP_COMMENT_TYPE">SP_COMMENT_TYPE</option> <option value="UP_KEYWORDS">UP_KEYWORDS</option> <option value="UP_SEQ_FEATURE">UP_SEQ_FEATURE</option> </param> <param name="Gene_Ontology" type="select" display="checkboxes" multiple="true" label="Gene_Ontology"> <option value="GOTERM_BP_1">GOTERM_BP_1</option> <option value="GOTERM_BP_2">GOTERM_BP_2</option> <option value="GOTERM_BP_3">GOTERM_BP_3</option> <option value="GOTERM_BP_4">GOTERM_BP_4</option> <option value="GOTERM_BP_5">GOTERM_BP_5</option> <option value="GOTERM_BP_ALL">GOTERM_BP_ALL</option> <option value="GOTERM_BP_DIRECT">GOTERM_BP_DIRECT</option> <option value="GOTERM_BP_FAT" selected="True">GOTERM_BP_FAT</option> <option value="GOTERM_CC_1">GOTERM_CC_1</option> <option value="GOTERM_CC_2">GOTERM_CC_2</option> <option value="GOTERM_CC_3">GOTERM_CC_3</option> <option value="GOTERM_CC_4">GOTERM_CC_4</option> <option value="GOTERM_CC_5">GOTERM_CC_5</option> <option value="GOTERM_CC_ALL">GOTERM_CC_ALL</option> <option value="GOTERM_BP_DIRECT">GOTERM_BP_DIRECT</option> <option value="GOTERM_CC_1">GOTERM_CC_1</option> <option value="GOTERM_CC_2">GOTERM_CC_2</option> <option value="GOTERM_CC_3">GOTERM_CC_3</option> <option value="GOTERM_CC_4">GOTERM_CC_4</option> <option value="GOTERM_CC_5">GOTERM_CC_5</option> <option value="GOTERM_CC_ALL">GOTERM_CC_ALL</option> <option value="GOTERM_CC_FAT" selected="True">GOTERM_CC_FAT</option> <option value="GOTERM_MF_1">GOTERM_MF_1</option> <option value="GOTERM_MF_2">GOTERM_MF_2</option> <option value="GOTERM_MF_3">GOTERM_MF_3</option> <option value="GOTERM_MF_4">GOTERM_MF_4</option> <option value="GOTERM_MF_5">GOTERM_MF_5</option> <option value="GOTERM_MF_ALL">GOTERM_MF_ALL</option> <option value="GOTERM_MF_FAT" selected="True">GOTERM_MF_FAT</option> </param> <param name="General_Annotations" type="select" display="checkboxes" multiple="true" label="General_Annotations"> <option value="CHROMOSOME">CHROMOSOME</option> <option value="CYTOBAND">CYTOBAND</option> <option value="ENTREZ_GENE_SUMMARY">ENTREZ_GENE_SUMMARY</option> <option value="OFFICIAL_GENE_SYMBOL">OFFICIAL_GENE_SYMBOL</option> <option value="PIR_SUMMARY">PIR_SUMMARY</option> <option value="SP_COMMENT">SP_COMMENT</option> </param> <param name="Literature" type="select" display="checkboxes" multiple="true" label="Literature"> <option value="GENERIF_SUMMARY">GENERIF_SUMMARY</option> <option value="HIV_INTERACTION_PUBMED_ID">HIV_INTERACTION_PUBMED_ID</option> <option value="PUBMED_ID">PUBMED_ID</option> </param> <param name="Main_Accessions" type="select" display="checkboxes" multiple="true" label="Main_Accessions"> <option value="ENSEMBL_GENE_ID">ENSEMBL_GENE_ID</option> <option value="ENTREZ_GENE_ID">ENTREZ_GENE_ID</option> </param> <param name="Pathways" type="select" display="checkboxes" multiple="true" label="Pathways"> <option value="BBID">BBID</option> <option value="BIOCARTA">BIOCARTA</option> <option value="EC_NUMBER">EC_NUMBER</option> <option value="KEGG_PATHWAY" selected="True">KEGG_PATHWAY</option> <option value="REACTOME_PATHWAY">REACTOME_PATHWAY</option> </param> <param name="Protein_Domains" type="select" display="checkboxes" multiple="true" label="Protein_Domains"> <option value="GENE3D">GENE3D</option> <option value="INTERPRO">INTERPRO</option> <option value="PFAM">PFAM</option> <option value="PIR_SUPERFAMILY">PIR_SUPERFAMILY</option> <option value="PRINTS">PRINTS</option> <option value="PRODOM">PRODOM</option> <option value="PROSITE">PROSITE</option> <option value="SMART">SMART</option> <option value="SUPFAM">SUPFAM</option> <option value="TIGRFAMS">TIGRFAMS</option> </param> <param name="Protein_Interactions" type="select" display="checkboxes" multiple="true" label="Protein_Interactions"> <option value="BIOGRID_INTERACTION">BIOGRID_INTERACTION</option> <option value="DIP">DIP</option> <option value="HIV_INTERACTION">HIV_INTERACTION</option> <option value="HIV_INTERACTION_CATEGORY">HIV_INTERACTION_CATEGORY</option> <option value="INTACT">INTACT</option> <option value="MINT">MINT</option> <option value="UCSC_TFBS">UCSC_TFBS</option> </param> <param name="Tissue_Expression" type="select" display="checkboxes" multiple="true" label="Tissue_Expression"> <option value="CGAP_EST_QUARTILE">CGAP_EST_QUARTILE</option> <option value="CGAP_SAGE_QUARTILE">CGAP_SAGE_QUARTILE</option> <option value="GNF_U133A_QUARTILE">GNF_U133A_QUARTILE</option> <option value="UNIGENE_EST_QUARTILE">UNIGENE_EST_QUARTILE</option> <option value="UP_TISSUE">UP_TISSUE</option> </param> </when> <when value="without_AnnotationCategories"> </when> </conditional> <conditional name="FunctionalAnnotationCluster"> <param name="set_FACluster_params" type="select" label="Functional Annotation Clustering"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <when value="Yes"> <param name="overlap" type="integer" min="3" max="10" value="3" label="Similarity Term Overlap"/> <param name="kappa" type="select" label="Similarity Threshold"> <option value="20">0.20</option> <option value="25">0.25</option> <option value="30">0.30</option> <option value="35">0.35</option> <option value="40">0.40</option> <option value="45">0.45</option> <option value="50" selected="True">0.50</option> <option value="55">0.55</option> <option value="60">0.60</option> <option value="65">0.65</option> <option value="70">0.70</option> <option value="75">0.75</option> <option value="80">0.80</option> <option value="85">0.85</option> <option value="90">0.90</option> <option value="95">0.95</option> <option value="100">1.00</option> </param> <param name="initialSeed" type="integer" min="2" max="10" value="3" label="Initial Group Membership"/> <param name="finalSeed" type="integer" min="2" max="10" value="3" label="Initial Group Membership"/> <param name="linkage" type="select" label="Multiple Linkage Threshold"> <option value="0.0">0.00</option> <option value="0.05">0.05</option> <option value="0.10">0.10</option> <option value="0.15">0.15</option> <option value="0.20">0.20</option> <option value="0.25">0.25</option> <option value="0.30">0.30</option> <option value="0.35">0.35</option> <option value="0.40">0.40</option> <option value="0.45">0.45</option> <option value="0.50" selected="True">0.50</option> <option value="0.55">0.55</option> <option value="0.60">0.60</option> <option value="0.65">0.65</option> <option value="0.70">0.70</option> <option value="0.75">0.75</option> <option value="0.80">0.80</option> <option value="0.85">0.85</option> <option value="0.90">0.90</option> <option value="0.95">0.95</option> <option value="1.0">1.00</option> </param> </when> <when value="No"> </when> </conditional> <conditional name="FunctionalAnnotationChart"> <param name="set_FAChart_params" type="select" label="Functional Annotation Chart"> <option value="Yes">Yes</option> <option value="No" selected="True">No</option> </param> <when value="Yes"> <param name="count" type="integer" label="Count" value="2" /> <param name="threshold" type="float" label="EASE" value="0.1" /> </when> <when value="No"> </when> </conditional> <conditional name="FunctionalAnnotationTable"> <param name="set_FATable_params" type="select" label="Functional Annotation Table"> <option value="Yes">Yes</option> <option value="No" selected="True">No</option> </param> <when value="Yes"> </when> <when value="No"> </when> </conditional> <conditional name="GeneListReport"> <param name="set_GLReport_params" type="select" label="Gene List Report"> <option value="Yes">Yes</option> <option value="No" selected="True">No</option> </param> <when value="Yes"> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data name="output1" format="tabular" label="${tool.name} on ${on_string}: Functional Annotation Cluster"> <filter>FunctionalAnnotationCluster['set_FACluster_params'] == 'Yes'</filter> </data> <data name="output2" format="tabular" label="${tool.name} on ${on_string}: Functional Annotation Chart"> <filter>FunctionalAnnotationChart['set_FAChart_params'] == 'Yes'</filter> </data> <data name="output3" format="tabular" label="${tool.name} on ${on_string}: Functional Annotation Table"> <filter>FunctionalAnnotationTable['set_FATable_params'] == 'Yes'</filter> </data> <data name="output4" format="tabular" label="${tool.name} on ${on_string}: Gene List Report"> <filter>GeneListReport['set_GLReport_params'] == 'Yes'</filter> </data> </outputs> <tests> <test> <param name="input1" value="demolist1" ftype="tabular"/> <param name="identifier1" value="AFFYMETRIX_3PRIME_IVT_ID"/> <param name="email" value="yes"/> <conditional name="AnnotationCategories"> <param name="setAnnotationCategories" value="with_AnnotationCategories"/> <param name="Disease" value="GAD_DISEASE,GAD_DISEASE_CLASS,OMIM_DISEASE"/> <param name="Gene_Ontology" value="GOTERM_MF_FAT,GOTERM_CC_FAT,GOTERM_BP_FAT"/> <param name="Pathways" value="KEGG_PATHWAY"/> </conditional> <conditional name="FunctionalAnnotationCluster"> <param name="set_FACluster_params" value="Yes"/> </conditional> <conditional name="FunctionalAnnotationChart"> <param name="set_FAChart_params" value="Yes"/> </conditional> <conditional name="FunctionalAnnotationTable"> <param name="set_FATable_params" value="Yes"/> </conditional> <conditional name="GeneListReport"> <param name="set_GLReport_params" value="Yes"/> </conditional> <output name="output1"> <assert_contents> <has_text_matching expression="Annotation Cluster 1	Enrichment Score: \d*\.*\d*"/> </assert_contents> </output> <output name="output2"> <assert_contents> <has_line_matching expression="Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR"/> </assert_contents> </output> <output name="output3"> <assert_contents> <has_line_matching expression="ID	Gene Name	Species	BBID	BIOCARTA	COG_ONTOLOGY	GOTERM_BP_DIRECT	GOTERM_CC_DIRECT	GOTERM_MF_DIRECT	INTERPRO	KEGG_PATHWAY	OMIM_DISEASE	PIR_SUPERFAMILY	SMART	UP_KEYWORDS	UP_SEQ_FEATURE"/> </assert_contents> </output> <output name="output4"> <assert_contents> <has_line_matching expression="ID	Name	Species"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** Retrieve data from the Database for Annotation, Visualization and Integrated Discovery (DAVID) using Web Services into R objects. This tool offers the main functionalities of DAVID website including: i) user-friendly connectivity to upload gene/background list/s, change gene/background position ii) Reports of the submitted Gene List, Gene/Term Clusters, Functional Annotation Chart, Functional Annotation Table **Links and registration** http://david.abcc.ncifcrf.gov/ and https://bioconductor.org/packages/release/bioc/html/RDAVIDWebService.html The used e-mail address has to be registered at https://david.ncifcrf.gov/webservice/register.htm in order to get access to DAVID (WebService) ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btt487</citation> <citation type="doi">10.1038/nprot.2008.211</citation> </citations> </tool>