diff ImportDataFromMatrix.xml @ 0:1024245abc70 draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ImportDataFromMatrix.xml	Thu Feb 22 08:38:22 2018 -0500
@@ -0,0 +1,94 @@
+<tool id="importMatrixData" name="Import custom data" version="1.0.0">
+
+    <description>Quality control and normalization of a custom matrix expression data</description>
+
+    <requirements>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">bioconductor-geometadb</requirement>
+        <requirement type="package">bioconductor-limma</requirement>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">bioconductor-affyplm</requirement>
+        <requirement type="package">r-jsonlite</requirement>
+        <requirement type="package">r-dplyr</requirement>
+        <requirement type="package">r-optparse</requirement>
+     </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <regex match="Warning" source="both" level="warning"/>
+    </stdio>
+
+    <command>
+        <![CDATA[ 
+        Rscript --vanilla 
+        ${__tool_directory__}/ImportDataFromMatrix.R
+            --input $input
+            --normalization $normalization
+            --conditions $conditions
+            --annotations $annotations
+            --rdataoutput $result_export_eset
+            --htmloutput $result_html
+            --htmloutputpath $result_html.files_path
+            --htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html
+        ]]>
+        </command>
+
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
+        <param name="normalization" type="select" label="Preprocessing/normalization">
+            <option value="quantile">quantile normalization + log2</option>
+            <option value="log2">log2 only</option>
+            <option value="none">none</option>
+        </param>
+        <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
+        <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>		
+    </inputs>
+
+    <outputs>
+        <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
+        <data format="html" name="result_html" label="QC result"/>
+    </outputs>
+
+    <help>
+<![CDATA[ 
+**What it does**
+		     	
+This tool imports data stored in a tabular text file. 
+Column titles (chip IDs) must match the IDs of the .cond file.
+GPL annotation code is also required to fetch annotations from GEO.
+
+**Exemple**
+
+Header of input tabular text file
+::
+
+
+""	"GSM80460"	"GSM80461"	"GSM80462"	"GSM80463"	"GSM80464"
+"1007_s_at"	-0.0513991525066443	0.306845500314283	0.0854246562526777	-0.142417044615852	0.0854246562526777
+"1053_at"	-0.187707155126729	-0.488026018218199	-0.282789700980404	0.160920188181103	0.989865622866287
+"117_at"	0.814755482809874	-2.15842936260448	-0.125006361067033	-0.256700472111743	0.0114956388378294
+"121_at"	-0.0558912008920451	-0.0649174766813385	0.49467161164755	-0.0892673380970874	0.113700499164728
+"1294_at"	0.961993677420255	-0.0320936297098533	-0.169744675832317	-0.0969617298870879	-0.181149439104566
+"1316_at"	0.0454429707611671	0.43616183931445	-0.766111939825723	-0.182786075741673	0.599317793698226
+"1405_i_at"	2.23450132056221	0.369606070031838	-1.06190243892591	-0.190997225060914	0.595503660502742
+
+
+The .cond file should look like this 
+::
+
+ GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
+ GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
+ GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors
+ GSM80476	series of 4 normals	GSM80476 OSCE-2N Series of 4 Normals
+ GSM80477	series of 4 normals	GSM80477 OSCE-9N Series of 4 Normals
+
+				
+**Results**
+	- Boxplots and MA plots 
+	- Rdata object containing the data for further analysis.
+]]>
+    </help>
+
+</tool>