diff getMutationType.xml @ 0:0475e4175855 draft default tip

planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getMutationType.xml	Mon Apr 30 05:25:11 2018 -0400
@@ -0,0 +1,38 @@
+<tool id="getMutationType" name="Get specific types of mutations">
+  <description></description>
+  <command interpreter="perl">
+	/home/galaxy/tools/CTK/getMutationType.pl -mutationType $mutationType $input_tag_uniq_mutation_txt $output_tag_uniq_bed
+  </command>
+
+  <inputs>
+        <param name="mutationType" type="select" label="Select a specific type of mutations ">
+                <option value="deletion">deletion</option>
+		<option value='substitution'>substitution</option>
+                <option value="insertion">insertion</option>
+        </param>
+        <param name="input_tag_uniq_mutation_txt" type="data" format="tabular" label="Input file in tabular format of unique mutations"/>
+  </inputs>
+  
+  <outputs>
+	<data name="output_tag_uniq_bed" format="bed" label="Get ${mutationType.value_label} mutation type on ${on_string}">
+        </data>
+  </outputs>
+
+  <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Get specific types of mutations, such as deletions, substitutions, and insertions around the cross-linked mutation site. 
+
+-----
+
+**Substitutions, deletions, and insertions**
+
+Based on the analysis performed so far on Nova, brPTB, Hu CLIP experiments, it appears that only deletions represent bona fide cross-linking induced mutations, while substitutions are mostly (if not all) due to sequencing/alignment errors, polymorphisms, or (potentially) RNA editing. It is estimated that ~7-25% of CLIP tags harbor deletion sites, frequently overlapping the binding motif. Therefore, it is highly recommended to do separate analysis of different types of mutations.
+
+However, it is not excluded that different proteins might differ due to the nature of amino-acid-nucleotide interaction and cross-linking. Therefore, analysis of more proteins will be very interesting.
+
+  </help>
+</tool>