Mercurial > repos > taoufik > microarrays
diff query_microarray_datasets/Get_Datasets.xml @ 1:842f8effaf59 draft default tip
Deleted selected files
| author | taoufik |
|---|---|
| date | Thu, 27 Dec 2018 06:56:28 -0500 |
| parents | cf862e6a6ddb |
| children |
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--- a/query_microarray_datasets/Get_Datasets.xml Thu Dec 27 05:54:24 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ -<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>