<tool id="sequence_format_converter" name="sequence_format_converter" version="2.1.0">
  <description></description>
  <command><![CDATA[
    #if $input.is_of_type('fastq.gz'):
      gzip -dc $input > '${input}.tmp';
      python '$__tool_directory__'/sequence_format_converter.py
      --input '${input}.tmp'
      --output '$output'
      --format '$output_format';
      rm '${input}.tmp';
    #else:
      python '$__tool_directory__'/sequence_format_converter.py
      --input '$input'
      --output '$output'
      --format '$output_format'
    #end if
  ]]></command>

<inputs>
    <param name="input" type="data" format="fasta, fastq, tabular" label="file to convert to tabular (input format is automatically detected)"/>
    <param name="output_format" type="select" label="conversion options">
        <option value="tabular" selected="true">tabular</option>
        <option value="fasta">Fasta</option>
        <option value="fastaw">Weighted fasta</option>
    </param>
   </inputs>

 <outputs>
   <data format="fasta" name="output" label="${output_format} conversion of ${input.name}">
     <change_format>
        <when input="output_format" value="tabular" format="tabular"/>
     </change_format>
   </data>
</outputs>

    <tests>
        <test>
            <!-- convertion fasta to tabular -->
            <param name="output_format" value="tabular" />
            <param ftype="fasta" name="input" value="input.fa" />
            <output file="output.tab" name="output" />
        </test>
        <test>
            <!-- convertion tabular to fasta -->
            <param name="output_format" value="fasta" />
            <param ftype="tabular" name="input" value="output.tab" />
            <output file="input.sorted.fa" name="output" sort="True"/>
        </test>
        <test>
            <!-- convertion fastaw to tabular -->
            <param name="output_format" value="tabular" />
            <param ftype="fasta" name="input" value="output.faw" />
            <output file="output.sorted.tab" name="output" sort="True"/>
        </test>
        <test>
            <!-- convertion tabular to fastaw -->
            <param name="output_format" value="fastaw" />
            <param ftype="tabular" name="input" value="output.tab" />
            <output file="output.sorted.faw" name="output" sort="True" />
        </test>
         <test>
            <!-- convertion fasta to fastaw -->
            <param name="output_format" value="fastaw" />
            <param ftype="fasta" name="input" value="input.fa" />
            <output file="output.sorted.faw" name="output" sort="True" />
        </test>
        <test>
            <!-- convertion fastaw to fasta -->
            <param name="output_format" value="fasta" />
            <param ftype="fasta" name="input" value="output.faw" />
            <output file="input.sorted.fa" name="output" sort="True" />
        </test>
        <test>
            <!-- convertion fastq to tabular -->
            <param name="output_format" value="tabular" />
            <param ftype="fastq" name="input" value="input.fastqsanger" />
            <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
        </test>
         <test>
            <!-- convertion fastq to fasta -->
            <param name="output_format" value="fasta" />
            <param ftype="fasta" name="input" value="input.fastqsanger" />
            <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
        </test>
        <test>
            <!-- convertion fastq to fastaw -->
            <param name="output_format" value="fastaw" />
            <param ftype="fasta" name="input" value="input.fastqsanger" />
            <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
        </test>
        <test>
            <!-- convertion fastq.gz to tabular -->
            <param name="output_format" value="tabular" />
            <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
            <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
        </test>
         <test>
            <!-- convertion fastq.gz to fasta -->
            <param name="output_format" value="fasta" />
            <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
            <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
        </test>
        <test>
            <!-- convertion fastq.gz to fastaw -->
            <param name="output_format" value="fastaw" />
            <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
            <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
        </test>
   </tests>


<help>

**What it does**

The tool performs all pairwise conversions between sequence formats fasta, fastaw and tabular.

The tool is also able to convert fastq format in any of the formats fasta, fastaw and tabular.

The format of the input is automatically detected by the tool.

**Formats**

*Fasta*

>id1

ATGCATGACCAGATAGGAC

>id2

ATGCATGACCAGATAGGAC

Note that the tool handles fasta sequences over multiple lines


----------

*Fastaw*

Allows to reduce the size of a fasta file of sequence reads:

>id1_n1

ATGCATGACCAGATAGGAC

>id2_n2

ATGCATGACCAGATAGGAC

etc...

Here n1 and n2 are integers that indicate the number of reads of the sequence found in the sequencing dataset

Note that if 2 fastaw files are merged (e.g. by concatenation), the values of the number of reads are wrong.

These values can simply be re-computed by submitting the merged file to a fastaw conversion with the *sequence_format_converter* tool !


----------

*Tabular*

Is a tabular version of fastaw without fasta headers:

column 1               column2

ATGCATGACCAGATAGGAC    n1

ATGCATGACCAGATAGGAC    n2


----------

*Fastq*

@HWI-1

ATGCATGACCAGATAGGAC

\+

BBBA;ACB9ABCBABB@@/

@HWI-2

ATGCATGACCAGATAGGAC

\+

?03@?82?B>C@B>@CC?0


</help>

</tool>