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changeset 1:842f8effaf59 draft default tip

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Deleted selected files
author taoufik
date Thu, 27 Dec 2018 06:56:28 -0500
parents cf862e6a6ddb
children
files query_microarray_datasets/GetDatasets.R query_microarray_datasets/Get_Datasets.xml query_microarray_datasets/images/workflow.jpg
diffstat 3 files changed, 0 insertions(+), 124 deletions(-) [+]
line wrap: on
line diff
--- a/query_microarray_datasets/GetDatasets.R	Thu Dec 27 05:54:24 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-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.')
-    }
-  }
-}
-
--- 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&lt;name&gt;.*)" 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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