galaxy/tools/next_gen_conversion/fastq_conversions.xml

<tool id="fastq_conversions" name="FASTQ Conversions" version="1.0.0">
  <description>converts between FASTQ data and other data formats</description>
  <command interpreter="python">
    fastq_conversions.py 
    --command=$conversionType.type
    --input=$input
    #if $conversionType.type == "sol2std":
     --outputFastqsanger=$outputFastqsanger
    #else:
     --outputFastqsanger="None"
    #end if
    #if $conversionType.type == "std2sol":
     --outputFastqsolexa=$outputFastqsolexa
    #else:
     --outputFastqsolexa="None"
    #end if
    #if $conversionType.type == "fq2fa":
     --outputFasta=$outputFasta
    #else:
     --outputFasta="None"
    #end if
  </command>
  <inputs>
    <conditional name="conversionType">
      <param name="type" type="select" label="What type of conversion do you want to do?">
        <option value="sol2std">Solexa/Illumina FASTQ to standard Sanger FASTQ</option>
        <option value="std2sol">Standard Sanger FASTQ to Solexa/Illumina FASTQ</option>
        <option value="fq2fa">Various FASTQ to FASTA</option>
      </param>
      <when value="sol2std">
        <param name="input" type="data" format="fastqsolexa" label="File to convert" />
      </when>
      <when value="std2sol">
        <param name="input" type="data" format="fastqsanger" label="File to convert" />
      </when>
      <when value="fq2fa">
        <param name="input" type="data" format="fastqsolexa, fastqsanger" label="File to convert" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="outputFastqsanger" format="fastqsanger">
      <filter>conversionType['type'] == 'sol2std'</filter>
    </data>
    <data name="outputFastqsolexa" format="fastqsolexa">
      <filter>conversionType['type'] == 'std2sol'</filter>
    </data>
    <data name="outputFasta" format="fasta">
      <filter>conversionType['type'] == 'fq2fa'</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="type" value="sol2std" />
      <param name="input" value="fastq_conv_in1.fastq" ftype="fastqsolexa" />
      <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" />
    </test>
    <test>
      <param name="type" value="std2sol" />
      <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
      <output name="outputFastqsolexa" file="fastq_conv_out2.fastqsolexa" />
    </test>
    <test>
      <param name="type" value="fq2fa" />
      <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
      <output name="outputFasta" file="fastq_conv_out4.fasta" />
    </test>
  </tests>
  <help>
**What it does**

This tool offers several conversions options relating to the FASTQ format. 

-----

**Examples**

- Converting the Solexa/Illumina FASTQ data::

	@081017-and-081020:1:1:1715:1759
	GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
	+
	II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&amp;&amp;B

- will produce the following Sanger FASTQ data::

	@081017-and-081020:1:1:1715:1759
	GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
	+
	++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
	
- Converting standard Sanger FASTQ::
    
    @1831_573_1004/1
	AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
	+
	>&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
	@1831_573_1050/1
	TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
	+
	;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'1,

- will produce the following Solexa/Illumina FASTQ data::

	@1831_573_1004/1
	AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
	+
	][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
	@1831_573_1050/1
	TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
	+
	Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK

- Converting the Sanger FASTQ data::

    @1831_573_1004/1
	AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
	+
	>&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
	@1831_573_1050/1
	TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
	+
	;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'1,
	
- will produce the following FASTA data::

	>1831_573_1004/1
	AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
	>1831_573_1050/1
	TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT

  </help>
</tool>