Mercurial > repos > czouaoui > gc_cover_data

changeset 22:a1f6c322aa26 draft

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Uploaded
author czouaoui
date Wed, 16 May 2018 10:12:05 -0400
parents 514a2b9d8e2e
children 8a780635d8b4
files gc_cover_data/gc_cover_data.xml
diffstat 1 files changed, 26 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gc_cover_data/gc_cover_data.xml	Wed May 16 10:12:05 2018 -0400
@@ -0,0 +1,26 @@
+<tool id="gc_cover_data" name="Generating R Data to run GC Cover Shiny app inside Galaxy" version="0.1.0">
+		<requirements>
+			<requirement type="package" version="2.46.0">bioconductor-biostrings</requirement>
+		</requirements>
+    <command detect_errors="exit_code"><![CDATA[
+				Rscript $__tool_directory__/getGCCoverData.R $input1 $input2 "$input1.name"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fasta" label="DNA Sequence"/>
+				<param type="data" name="input2" format="txt" label="Coverage (Imagesmajik file)"/>
+    </inputs>
+    <outputs>
+        <data name= "output" format="rdata" label="${input1.name} - GCCover" from_work_dir="gcCover.RData"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="fasta" value="sequence.fasta"/>
+						<param name="input2" format="txt" value="covFile"/>
+            <output name="output" format="rdata" file="gcCover.RData"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool is used to generate a R Data file from Fasta and Imagesmajik files. The data inside this file are used
+				to start the GC Cover Shiny application from Galaxy.
+    ]]></help>
+</tool>