view convert_bc_to_binary_RY.xml @ 19:885602df4554 draft

another try with bedtools dependency

<tool id="convert_bc_to_binary_RY.py" name="Create binary barcodes" version="0.1.0">
  <description>from regular barcodes.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <version_command>python convert_bc_to_binary_RY.py --version</version_command>
  <command interpreter="python"><![CDATA[
convert_bc_to_binary_RY.py
#if $positional_1 and $positional_1 is not None:
$positional_1
#end if
> $default]]></command>
  <inputs>
    <param label="Fastq file to convert." name="positional_1" type="data" format="fastq"/>
  </inputs>
  <outputs>
    <data hidden="false" name="default" format="fastq"/>
  </outputs>
  <tests>
    <test>
      <param name="positional_1" value="extracted_bcs.fastq"/>
      <output name="default" file="converted_bcs.fastq"/>
    </test>
  </tests>
  <help><![CDATA[

**What it does**

This tool converts standard nucleotides to IUPAC nucleotide codes used for binary barcodes.
A and G are converted to nucleotide code R. T, U and C are converted to Y.

**Input**

The input for this tool is a fastq file.

**Output**

This tool produces a single fastq file containing the converted barcodes.

** References **
]]></help>
  <expand macro="citations" />
</tool>