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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rdavidwebservice commit b664316c8917dff50de40207c2b3104ed850b90b |
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macros.xml rdavidwebservice.xml test-data/demolist1 |
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| diff -r 000000000000 -r 5aa52484bef2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 23 13:44:50 2019 -0400 |
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| @@ -0,0 +1,44 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.20.0</token> + <xml name="identifier_options"> + <option value="AFFYMETRIX_3PRIME_IVT_ID">AFFYMETRIX_3PRIME_IVT_ID</option> + <option value="AFFYMETRIX_EXON_ID">AFFYMETRIX_EXON_ID</option> + <option value="AGILENT_CHIP_ID">AGILENT_CHIP_ID</option> + <option value="AGILENT_ID">AGILENT_ID</option> + <option value="AGILENT_OLIGO_ID">AGILENT_OLIGO_ID</option> + <option value="APHIDBASE_ID">APHIDBASE_ID</option> + <option value="BEEBASE_ID">BEEBASE_ID</option> + <option value="BEETLEBASE_ID">BEETLEBASE_ID</option> + <option value="BGD_ID">BGD_ID</option> + <option value="CGNC_ID">CGNC_ID</option> + <option value="CRYPTODB_ID">CRYPTODB_ID</option> + <option value="DICTYBASE_ID">DICTYBASE_ID</option> + <option value="ENSEMBL_GENE_ID">ENSEMBL_GENE_ID</option> + <option value="ENSEMBL_TRANSCRIPT_ID">ENSEMBL_TRANSCRIPT_ID</option> + <option value="ENTREZ_GENE_ID" selected="True">ENTREZ_GENE_ID</option> + <option value="FLYBASE_GENE_ID">FLYBASE_GENE_ID</option> + <option value="GENBANK_ACCESSION">GENBANK_ACCESSION</option> + <option value="GENOMIC_GI_ACCESSION">GENOMIC_GI_ACCESSION</option> + <option value="GENPEPT_ACCESSION">GENPEPT_ACCESSION</option> + <option value="LOCUS_TAG">LOCUS_TAG</option> + <option value="MGI_ID">MGI_ID</option> + <option value="MIRBASE_ID">MIRBASE_ID</option> + <option value="MRNA_GI_ACCESSION">MRNA_GI_ACCESSION</option> + <option value="NASONIABASE_ID">NASONIABASE_ID</option> + <option value="PROTEIN_GI_ACCESSION">PROTEIN_GI_ACCESSION</option> + <option value="PSEUDOCAP_ID">PSEUDOCAP_ID</option> + <option value="REFSEQ_MRNA">REFSEQ_MRNA</option> + <option value="REFSEQ_PROTEIN">REFSEQ_PROTEIN</option> + <option value="RGD_ID">RGD_ID</option> + <option value="SGD_ID">SGD_ID</option> + <option value="TAIR_ID">TAIR_ID</option> + <option value="UNIGENE">UNIGENE</option> + <option value="UNIPROT_ACCESSION">UNIPROT_ACCESSION</option> + <option value="UNIPROT_ID">UNIPROT_ID</option> + <option value="VECTORBASE_ID">VECTORBASE_ID</option> + <option value="WORMBASE_GENE_ID">WORMBASE_GENE_ID</option> + <option value="XENBASE_ID">XENBASE_ID</option> + <option value="ZFIN_ID">ZFIN_ID</option> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 5aa52484bef2 rdavidwebservice.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdavidwebservice.xml Thu May 23 13:44:50 2019 -0400 |
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| b'@@ -0,0 +1,372 @@\n+<tool id="rdavidwebservice" name="RDAVIDWebService" version="@TOOL_VERSION@">\n+ <description>\n+ Run functional annotation using DAVID \n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">bioconductor-rdavidwebservice</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+cat \'$script\' &&\n+Rscript \'$script\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="script"><![CDATA[\n+## Setup R error handling to go to stderr\n+options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})\n+## Unify locale settings\n+loc <- Sys.setlocale("LC_MESSAGES", "C.UTF-8")\n+## Import libraries\n+library(RDAVIDWebService)\n+\n+gene_list <- scan(\'$input1\', what="character")\n+gene_identifier_type <- \'$identifier1\'\n+\n+#if str(\'$__user_email__\') != "":\n+email <- \'$__user_email__\'\n+#else:\n+email <- \'galaxy_user@galaxy.org\'\n+#end if\n+\n+david <- DAVIDWebService(email=email, url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/")\n+\n+geneList <- addList(david, gene_list, idType=gene_identifier_type,\n+ listName="genelist", listType="Gene")\n+\n+#if str($background.background_selector) == "with_background":\n+background_list <- scan(\'$background.input2\', what="character")\n+background_identifier_type <- \'$background.identifier2\'\n+background <- addList(david, background_list, idType=background_identifier_type,\n+ listName="backgroundlist",listType="Background")\n+#end if\n+\n+#if str($AnnotationCategories.setAnnotationCategories) == "Yes": \n+annocategories <- c(\'$AnnotationCategories.Disease\', \'$AnnotationCategories.Functional_Categories\', \'$AnnotationCategories.Gene_Ontology\', \'$AnnotationCategories.General_Annotations\', \'$AnnotationCategories.Literature\', \'$AnnotationCategories.Main_Accessions\', \'$AnnotationCategories.Pathways\', \'$AnnotationCategories.Protein_Domains\', \'$AnnotationCategories.Tissue_Expression\')\n+annocategories <- annocategories[annocategories != \'None\']\n+annocategories <- unlist(strsplit(annocategories, split = ",")) \n+setAnnotationCategories(david, annocategories)\n+#end if\n+\n+#if str($FunctionalAnnotationCluster.set_FACluster_params) == "Yes": \n+getClusterReportFile(david, \'$output1\', \n+ kappa = as.integer(\'$FunctionalAnnotationCluster.kappa\'), \n+ overlap = as.integer(\'$FunctionalAnnotationCluster.overlap\'), \n+ initialSeed = as.integer(\'$FunctionalAnnotationCluster.initialSeed\'), \n+ finalSeed = as.integer(\'$FunctionalAnnotationCluster.finalSeed\'), \n+ linkage = as.double(\'$FunctionalAnnotationCluster.linkage\'))\n+#end if\n+\n+#if str($FunctionalAnnotationChart.set_FAChart_params) == "Yes" : \n+getFunctionalAnnotationChartFile(david, \'$output2\', \n+ count = as.integer(\'$FunctionalAnnotationChart.count\'), \n+ threshold = as.double(\'$FunctionalAnnotationChart.threshold\'))\n+#end if \n+\n+#if str($FunctionalAnnotationTable.set_FATable_params) == "Yes": \n+getFunctionalAnnotationTableFile(david, \'$output3\')\n+#end if \n+\n+#if str($GeneListReport.set_GLReport_params) == "Yes": \n+getGeneListReportFile(david, \'$output4\')\n+#end if \n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="input1" type="data" format="txt" label="Select gene list"/>\n+ <param name="identifier1" type="select" label="Select gene list identifier type">\n+ <expand macro="identifier_options" />\n+ </param>\n+ <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)">\n+ <validator type="regex" message="You need to agree the terms to continue by typing \''..b'ter>FunctionalAnnotationChart[\'set_FAChart_params\'] == \'Yes\'</filter>\n+ </data>\n+ <data name="output3" format="tabular" label="${tool.name} on ${on_string}: Functional Annotation Table">\n+ <filter>FunctionalAnnotationTable[\'set_FATable_params\'] == \'Yes\'</filter>\n+ </data>\n+ <data name="output4" format="tabular" label="${tool.name} on ${on_string}: Gene List Report">\n+ <filter>GeneListReport[\'set_GLReport_params\'] == \'Yes\'</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input1" value="demolist1" ftype="tabular"/>\n+ <param name="identifier1" value="AFFYMETRIX_3PRIME_IVT_ID"/>\n+ <param name="email" value="yes"/>\n+ <conditional name="AnnotationCategories">\n+ <param name="setAnnotationCategories" value="with_AnnotationCategories"/>\n+ <param name="Disease" value="GAD_DISEASE,GAD_DISEASE_CLASS,OMIM_DISEASE"/>\n+ <param name="Gene_Ontology" value="GOTERM_MF_FAT,GOTERM_CC_FAT,GOTERM_BP_FAT"/>\n+ <param name="Pathways" value="KEGG_PATHWAY"/>\n+ </conditional>\n+ <conditional name="FunctionalAnnotationCluster">\n+ <param name="set_FACluster_params" value="Yes"/>\n+ </conditional> \n+ <conditional name="FunctionalAnnotationChart">\n+ <param name="set_FAChart_params" value="Yes"/>\n+ </conditional>\n+ <conditional name="FunctionalAnnotationTable">\n+ <param name="set_FATable_params" value="Yes"/>\n+ </conditional>\n+ <conditional name="GeneListReport">\n+ <param name="set_GLReport_params" value="Yes"/>\n+ </conditional>\n+ <output name="output1">\n+ <assert_contents>\n+ <has_text_matching expression="Annotation Cluster 1	Enrichment Score: \\d*\\.*\\d*"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output2">\n+ <assert_contents>\n+ <has_line_matching expression="Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output3">\n+ <assert_contents>\n+ <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"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output4">\n+ <assert_contents>\n+ <has_line_matching expression="ID	Name	Species"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+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: \n+\n+i) user-friendly connectivity to upload gene/background list/s, change gene/background position \n+\n+ii) Reports of the submitted Gene List, Gene/Term Clusters, Functional Annotation Chart, Functional Annotation Table\n+\n+\n+**Links and registration**\n+\n+http://david.abcc.ncifcrf.gov/ and\n+https://bioconductor.org/packages/release/bioc/html/RDAVIDWebService.html\n+\n+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)\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btt487</citation>\n+ <citation type="doi">10.1038/nprot.2008.211</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 5aa52484bef2 test-data/demolist1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demolist1 Thu May 23 13:44:50 2019 -0400 |
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