diff countmatrixforedger.xml @ 0:c5a812cdf478 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/countmatrixforedger.xml	Fri Dec 09 10:52:35 2016 -0500
@@ -0,0 +1,95 @@
+<tool id="countmatrixforedger" name="countMatrixForEdger" version="1.0">
+    <description>Make a count matrix for edgeR</description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+        <![CDATA[ 
+            #for $i, $s in enumerate( $sample )#
+                echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data;
+            #end for#
+
+            cat script.data > /tmp/script.data;
+            $__tool_directory__/tools/scrsh.sh script.data;
+
+            cat count.matrix > $count_matrix;
+            cat annotation > $annotation;
+            cat script.log > $log;
+            cat error.log > $error_log
+
+        ]]>
+    </command>
+    <inputs>
+        <repeat name="sample" title="">
+            <param name="sample_data" type="data" format="data" label="" help="" />
+            <param name="sample_name" type="text" label="" help="" />
+            <param name="sample_group" type="text" label="" help="" />
+        </repeat>
+    </inputs>
+    <outputs>
+<!--        <data name="output" format="data" /> -->
+        <data name="count_matrix" format="data" />
+        <data name="annotation" format="data" />
+        <data name="log" format="data" />
+        <data name="error_log" format="data" />
+    </outputs>
+    <tests>
+<!--         <test>
+            <param name="sample_0|sample_data" value="data1" />
+            <param name="sample_1|sample_data" value="data2" />
+            <param name="sample_2|sample_data" value="data3" />
+            <param name="sample_3|sample_data" value="data4" />
+            <param name="sample_0|sample_name" value="sample1" />
+            <param name="sample_1|sample_name" value="sample2" />
+            <param name="sample_2|sample_name" value="sample3" />
+            <param name="sample_3|sample_name" value="sample4" />            
+            <param name="sample_0|sample_group" value="gr1" />
+            <param name="sample_1|sample_group" value="gr1" />
+            <param name="sample_2|sample_group" value="gr2" />
+            <param name="sample_3|sample_group" value="gr2" />
+            <output name="output" file="output"/>
+
+        </test> -->
+        <test>
+            <param name="sample_0|sample_data" value="data1" />
+            <param name="sample_1|sample_data" value="data2" />
+            <param name="sample_2|sample_data" value="data3" />
+            <param name="sample_3|sample_data" value="data4" />
+            <param name="sample_0|sample_name" value="sample1" />
+            <param name="sample_1|sample_name" value="sample2" />
+            <param name="sample_2|sample_name" value="sample3" />
+            <param name="sample_3|sample_name" value="sample4" />            
+            <param name="sample_0|sample_group" value="gr1" />
+            <param name="sample_1|sample_group" value="gr1" />
+            <param name="sample_2|sample_group" value="gr2" />
+            <param name="sample_3|sample_group" value="gr2" />
+            <output name="count_matrix" file="count.matrix"/>
+            <output name="annotation" file="annotation"/>
+            <output name="log" file="script.log"/>
+            <output name="error_log" file="error.log"/>
+        </test>
+
+    </tests>
+    <help>
+        <![CDATA[ 
+
+tutaj cos bedzie
+     ]]>
+    </help>
+        <citations>
+        <citation type="bibtex">
+            @article{Berenger2014,
+              doi = {10.1186/1758-2946-6-23},
+              url = {http://dx.doi.org/10.1186/1758-2946-6-23},
+              year  = {2014},
+              publisher = {Springer Nature},
+              volume = {6},
+              number = {1},
+              pages = {23},
+              author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
+              title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
+              journal = {Journal of Cheminformatics}
+            }
+        </citation>
+    </citations>
+</tool>