diff plotheatmap.xml @ 0:c5a812cdf478 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotheatmap.xml	Fri Dec 09 10:52:35 2016 -0500
@@ -0,0 +1,57 @@
+<tool id="plotheatmap" name="plotheatmap" version="1.0">
+    <description>Make a count matrix for edgeR</description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+        <![CDATA[ 
+            $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log
+
+
+
+        ]]>
+    </command>
+    <inputs>
+        <param name="count_matrix" type="data" format="data" label=""/>
+        <param name="stats_matrix" type="data" format="data" label=""/>
+        <param name="log_fc" type="float" value="0.5" label=""/>
+        <param name="log_cpm" type="float" value="0.5" label=""/>
+        <param name="pvalue" type="float" value="0.5" label=""/>
+        <param name="fdr" type="float" value="0.5" label=""/>
+
+    </inputs>
+    <outputs>
+<!--        <data name="output" format="data" /> --> 
+       <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" >
+            <filter>(outftype == 'pdf')</filter>
+        </data>
+        <data name="rscript_log" format="data" />
+        <data name="rerror_log" format="data" />
+    </outputs>
+    <tests>
+
+        <test>
+            <param name="count_matrix" value="count.matrix"/>
+            <param name="stats_matrix" value="stats.data"/>
+            <param name="log_fc" value="1"/>
+            <param name="log_cpm" value="2"/>
+            <param name="pvalue" value="0.05"/>
+            <param name="fdr" value="0.1"/>
+<!--             <output name="output" file="done"/> -->
+            <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" />
+            <output name="rscript_log" file="rscript.log"/>
+            <output name="rerror_log" file="rerror.log"/>
+
+        </test>
+
+    </tests>
+    <help>
+        <![CDATA[ 
+
+tutaj cos bedzie
+     ]]>
+    </help>
+    <citations>
+        
+    </citations>
+</tool>
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