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

planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty

<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>