| Next changeset 1:842f8effaf59 (2018-12-27) |
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query_microarray_datasets/GetDatasets.R query_microarray_datasets/Get_Datasets.xml query_microarray_datasets/images/workflow.jpg |
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| diff -r 000000000000 -r cf862e6a6ddb query_microarray_datasets/GetDatasets.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/query_microarray_datasets/GetDatasets.R Thu Dec 27 05:54:24 2018 -0500 |
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| @@ -0,0 +1,27 @@ +log_file=file("Query_Geo_Database.log", open = "wt") +sink(log_file) +sink(log_file, type = "out") +suppressWarnings(suppressMessages(library("batch"))) +suppressWarnings(suppressMessages(library(GEOquery))) +listArguments = parseCommandArgs(evaluate=FALSE) +GeoCode=listArguments[["GeoCode"]] +GeoCode=toupper(GeoCode) +gethelp.df =tryCatch(eList <- getGEOSuppFiles(GeoCode), error = function(cond)"skip") +if(is.null(gethelp.df)){ + gethelp.df =tryCatch(eList <- getGEOSuppFiles(GeoCode), error = function(cond)"skip") +} +if(is.null(gethelp.df)){ + print('GeoCode with no raw data, choose another code or retry.') +}else{ + if(is.data.frame(gethelp.df)==TRUE){ + rawdata=rownames(eList)[grep('RAW',rownames(eList))][1] + untar(rawdata, exdir = 'CEL') + }else{ + if(gethelp.df=="skip"){ + print('Network Trouble Try Again Or Check your GeoCode') + }else{ + print('GeoCode with no raw data, choose another code or retry.') + } + } +} + |
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| diff -r 000000000000 -r cf862e6a6ddb query_microarray_datasets/Get_Datasets.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/query_microarray_datasets/Get_Datasets.xml Thu Dec 27 05:54:24 2018 -0500 |
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| @@ -0,0 +1,97 @@ +<tool id="Get_Datasets" name="Query GEO Database" version="20181028"> + <description> Query Gene Expression Omnibus (GEO) Database using accession code. </description> + <requirements> + <requirement type="package" version="3.4.1_0">r-base</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="2.42.0">bioconductor-geoquery</requirement> + </requirements> + <command> + <![CDATA[ + Rscript '$__tool_directory__/GetDatasets.R' GeoCode $GeoCode + ]]> + </command> + <inputs> + <param name="GeoCode" size="40" type="text" value="GSE50628" label="GEO accession" help="Gene Expression Omnibus (GEO) accession code"> + <sanitizer> + <valid initial="string.printable,string.digits"> + </valid> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="microarray" type="microarray" name="Geo Raw"> + <discover_datasets pattern="(?P<name>.*)" ext="microarray" format="microarray" type="microarray" visible="true" assign_primary_output="true" directory="CEL" /> + </data> + </outputs> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <help> + +.. class:: infomark + +**Authors** Bensellak Taoufik bensellak.taoufik@gmail.com, El Messaoudi Idrissi Mohcine mohcine.elmessaoudi@gmail.com , Ahmed Moussa ahmed.moussa2@gmail.com . + +--------------------------------------------------- + +================================================================== +Query Gene Expression Omnibus (GEO) Database. +================================================================== + +----------- +Description +----------- + +This tool is used for querying Gene Expression Omnibus Database. + +**GEO accession** + +GEO Accession code + +----------------- +Workflow position +----------------- + +**Upstream tools** + ++------------------------+------------------+--------+-----------+ +| Name | output file |format | parameter | ++========================+==================+========+===========+ +| NA | NA | NA | NA | ++------------------------+------------------+--------+-----------+ + + +**Downstream tools** + ++-----------------------------------------------+------------------------------------------------+------------+ +| Name | Output file | Format | ++===============================================+================================================+============+ +| Create Desig | DataSet.Design.tsv,DataSet.Informations.RData | tsv,RData | ++-----------------------------------------------+------------------------------------------------+------------+ + +----------- +Input files +----------- + ++---------------------------+------------+ +| Parameter : num + label | Format | ++===========================+============+ +| GEO accession | String | ++---------------------------+------------+ + +------------ +Output files +------------ + +**Set of raw samples** + +------------------------------ +General schema of the workflow +------------------------------ + +.. image:: ./workflow.jpg + :height: 800 + :width: 700 + + </help> +</tool> |
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