annotate space2underscore_readname.xml @ 13:35aedbe548b9 draft

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<tool id="space2underscore_readname" name="Read name modifier" version="1.0.0">
  <description>--change space to underscore in the read name column</description>
  <command interpreter="python">changespacetounderscore_readname.py  $input $output $column_n </command>

  <inputs>
    <param name="input" type="data" label="Select input" />
    <param name="column_n" type="integer" value="6" label="Select column to modify" />
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
    
  </outputs>
  <tests>
    <!-- Test data with valid values -->
    <test>
      <param name="input" value="samplefq.snoope"/>
      <param name="column_n" value="6"/>
      <output name="output" file="samplefq.snoope.new"/>
    </test>
    
  </tests>
  <help>


.. class:: infomark

**What it does**

The readname produced by the "STR detection" step may contain spaces instead of underscores, which will cause downstream tools that use space as a column delimiter to fail. This tool will help convert space to underscore.
If your input does not have spaces in readname column, this step can be skipped.

**Citation**

When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
 
**Input**

The input files can be any tab delimited file. 

If this tool is used in STR-FM for STRs profiling, it should be in the same format as output from **STR detection program**. This format contains **length of repeat**, **length of left flanking region**, **length of right flanking region**, **repeat motif**, **hamming (editing) distance**, **read name**, **read sequence**, **read quality score**

**Output**

The same as input format.


</help>
</tool>