diff experimental_design.xml @ 0:afe85eb6572e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/experimental_design.xml	Mon Aug 29 05:41:20 2016 -0400
@@ -0,0 +1,57 @@
+<tool id="experimentaldesign_igg" name="ExperimentalDesign" version="1.0">
+	<description> </description>
+	<command interpreter="bash">
+		experimental_design/experimental_design.sh 
+		#for $i, $f in enumerate($patients)
+            "$f.id"
+            #for $j, $g in enumerate($f.samples)
+            	${g.sample}
+            #end for
+		#end for
+		$out_file
+	</command>
+	<inputs>
+		<repeat name="patients" title="Patient" min="1" default="1">
+            <repeat name="samples" title="Sample" min="1" default="1">
+                <param name="sample" format="tabular" type="data" label="Sample to Process" />
+            </repeat>
+			<param name="id" type="text" label="ID" />
+		</repeat>
+	</inputs>
+	<outputs>
+		<data format="tabular" name="out_file"/>
+	</outputs>
+	<help>
+Takes the ARGalaxy proprietary format and merges several samples and/or patients together.
+	</help>
+ <citations>
+    <!-- Example of annotating a citation using a DOI. -->
+    <citation type="doi">10.1093/bioinformatics/btq281</citation>
+
+    <!-- Example of annotating a citation using a BibTex entry. -->
+    <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
+    author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky},
+    title = {An interior-point method for large-scale l1-regularized logistic regression},
+    journal = {Journal of Machine Learning Research},
+    year = {2007},
+    volume = {8},
+    pages = {1519-1555}
+    }</citation>
+  </citations>
+  <tests>
+    <test>
+      <param name="input" value="1.bed"/>
+      <param name="column" value="1"/>
+      <param name="order" value="ASC"/>
+      <param name="style" value="num"/>
+      <output name="out_file1" file="sort1_num.bed"/>
+    </test>
+    <test>
+      <param name="input" value="7.bed"/>
+      <param name="column" value="1"/>
+      <param name="order" value="ASC"/>
+      <param name="style" value="alpha"/>
+      <output name="out_file1" file="sort1_alpha.bed"/>
+    </test>
+  </tests>
+</tool>