diff tools/filters/catWrapper.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/catWrapper.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,79 @@
+<tool id="cat1" name="Concatenate datasets">
+    <description>tail-to-head</description>
+    <command interpreter="python">
+        catWrapper.py 
+        $out_file1 
+        $input1
+        #for $q in $queries
+            ${q.input2}
+        #end for
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset"/>
+        <repeat name="queries" title="Dataset">
+            <param name="input2" type="data" label="Select" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="input" metadata_source="input1"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed"/>
+            <param name="input2" value="2.bed"/>
+            <output name="out_file1" file="cat_wrapper_out1.bed"/>
+        </test>
+        <!--TODO: if possible, enhance the underlying test code to handle this test
+            the problem is multiple params with the same name "input2"
+        <test>
+            <param name="input1" value="1.bed"/>
+            <param name="input2" value="2.bed"/>
+            <param name="input2" value="3.bed"/>
+            <output name="out_file1" file="cat_wrapper_out2.bed"/>
+        </test>
+        -->
+    </tests>
+    <help>
+
+.. class:: warningmark
+
+**WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format. 
+
+-----
+
+**What it does**
+
+Concatenates datasets
+
+-----
+
+**Example**
+
+Concatenating Dataset::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+
+with Dataset1::
+
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+    
+and with Dataset2::
+
+    chr2  100000030  200000955  P  0  +
+    chr2  100000015  200000999  Q  0  +
+
+will result in the following::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+    chr2  100000030  200000955  P  0  +
+    chr2  100000015  200000999  Q  0  +
+
+    </help>
+</tool>