diff catWrapper.xml @ 0:cf750d0edbd8 draft

Imported from capsule None
author mvdbeek
date Tue, 03 Mar 2015 05:06:43 -0500
parents
children 1bf1794dfcf6
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/catWrapper.xml	Tue Mar 03 05:06:43 2015 -0500
@@ -0,0 +1,68 @@
+<tool id="cat_multiple" name="Concatenate multiple datasets" version="0.1">
+    <description>tail-to-head</description>
+    <command interpreter="python">
+        catWrapper.py 
+        $out_file1 
+        #for $file in $input
+            $file
+        #end for
+    </command>
+    <inputs>
+        <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format_source="input" metadata_source="input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="1.bed,2.bed"/>
+            <output name="out_file1" file="cat_wrapper_out1.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  +
+
+-----
+
+Adapted from the concatenate tool that comes with galaxy.
+    </help>
+</tool>